Unit #3 (Chemical Structure) 3-1

Chemical Structure
Electronic Structure of Atoms
READING: BLB-11, Ch. 6; Probs: 6, 16, 26, 38, 43, 44, 54, 56, 68, 74, 78, (94)
BLB-12, Ch. 6; Probs: 7, 18, 28, 40, 45, 46, 56, 58, 70, 74, 79, 84, (93)
PROBLEMS: 1-7

(1) Wave-Particle Duality for Light and Electrons

To study the electronic structure of atoms, that is, to determine how the electrons
distribute themselves in space around the positively charged nucleus, we must “shine
light on the atom.” Classical physics treats electrons and nuclei as particles which carry
mass (m: kg), can be identified at certain positions in space (x = (x, y, z); m) and move
with some speed (v; m/sec). Therefore, particles carry momentum (p = mv; kgm/sec)
and kinetic energy (K.E. = ½mv2; Joule = kgm2/sec2). Particles can be deflected, by
undergoing collisions.

Classical physics also treats light as waves, which are characterized by a frequency (:
sec–1), wavelength (: m), amplitude (A) and phase (). Waves travel with some speed,
which equals frequency  wavelength (m/sec); light waves travel at the speed of light c =
 = 3.00  108 m/sec. We represent waves by oscillating (periodic) functions; below is
a wave where the horizontal axis is position and the vertical axis is amplitude. The
wavelength is the distance between adjacent crests (troughs); the amplitude is the
maximum height (depth); the phase determines where it starts (its origin point). The
expression below the figure is for a traveling wave, which is a wave that moves (like
light) from left to right.


1.0

0.5 A
0.0

-0.5

-1.0

 2 x   2  x  ct  
Traveling wave: A cos   t     A cos    .
     

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At a specific point, x0, then,

 2 x0   2 ct 2 x0   2 ct 
A cos   t     A cos       A cos    0  . When
         
looking at the point x0, the wave’s amplitude oscillates as time passes (t).

Standing wave: two traveling waves moving in opposite directions.

 2 x   2 x   2 x 
A cos   t     A cos   t      2 A cos t  cos    ,
        
where the amplitude of the wave oscillates with time, but the wave, itself, does not move.

Light travels at constant speed: c = 3.0  108 m/s. So,  = c (a constant). The
electromagnetic spectrum (light) is divided into various sections:

Radiation  (m)  (sec–1) Comments

Gamma 10–11 (10 pm) 3  1019 Nuclear fission (splitting nuclei)
X-rays 10–9 (10 nm) 3  1017 Remove electrons from core levels of atoms;
high energy “ionization”
Ultraviolet 10–8 (10 nm) 3  1016 Remove electrons from valence levels of atoms
and molecules – “ionization”; OR move
electrons to higher energy levels in atoms or
molecules; can break chemical bonds
Visible 10–7 (100 nm) 3  1015 Move electrons to higher energy levels – create
molecules or atoms in “excited states”
Infrared 10–6 (1000 nm) 3  1014 Induce vibrations in molecules – stretching and
bending
Microwaves 10–2 (10 mm) 3  1010 Induce rotations of molecules – spinning
(30 GHz)
Radio 100 (1 m) 3  107 Energies too small to induce chemistry; BUT,
(30 MHz) energy changes between different nuclear “spin
states” – nuclear magnetic resonance (“MRI”)

During the late 1800’s and into the 1920’s, there were numerous physical problems that
could not be solved by classical ideas in physics:

(1) Photoelectric effect—light impinging on a metal surface can release electrons, light
behaves as a particle;
(2) Electron diffraction—moving electrons can be diffracted by a crystal, just like X-
rays, electrons behave as a wave;
(3) Blackbody radiation—when a solid body is heated, it will glow, and as the
temperature increases, the color changes until it becomes “white hot;”
(4) Atomic emission spectra—when elemental gases are subjected to a large voltage,
they emit light at distinct and discrete (not continuous) wavelengths.

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These problems (among others) led to the development of quantum mechanics. To

explain these phenomena, we must use Planck’s hypothesis (which is now an axiom in
the discipline of quantum mechanics) that electromagnetic radiation exists in quanta,
which means discrete quantities of energy:
E = h = hc/;

where Planck’s constant h = 6.63  10–34 Js. Each quantum of light is called a photon:
one photon has energy h; two photons have energy 2h; twenty photons have energy
20h; Avogadro’s number of photons has energy (6.02  1023)h. The intensity of light
(its brightness) is determined by the number of photons, not its frequency.

Problem: Calculate the energy, in kJ, of 1 photon and 1 mole of photons with a
wavelength of 240 nm. (UV)

(1 photon):
(6.63  1034 J  sec)(3.0  108 m / sec) 1 kJ
9
  8.29  10 22 kJ
(240  10 m) 1000 J
 
E of 1 photon

(1 mole):
(6.63  1034 J  sec)(3.0  108 m / sec) 1 kJ
(6.02  1023/mole) 9
  498 kJ/mol
(240  10 m) 1000 J
 
E of 1 photon

498 kJ is the amount of energy needed to break the bond in 1 mole of O2 molecules and
form two moles of O atoms:

h
O2   2O; needs 498 kJ/mol, or 1 mole of photons,
each with wavelength  = 240 nm.

Since light with wavelengths greater than 240 nm are less energetic, but light with
wavelengths less than 240 nm are more energetic, we call 240 nm the MAX for this
reaction. From a thermochemical point of view, we need at least 498 kJ to break apart 1
mole of O2 molecules. We can always use more energy than this. So, higher energy light
( < 240 nm) will also perform this process. Since O2 exists in the atmosphere, these
molecules will absorb sunlight in the UV for   240 nm: the molecules act as a filter for
this radiation.

de Broglie proposed (bravely) that since light showed particle-like character through the
photoelectric effect, perhaps particles (matter) could show wave-like character. This was
verified by electron diffraction. de Broglie described matter waves – wavelengths
associated with the motion of particles. One way of establishing the analogy stems from
Einstein’s ideas on relativity: E = mc2 = pc: light (as a photon) is a “particle” with no

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Unit #3 (Chemical Structure) 3-4

mass (m = 0), yet it has energy (h/)c. The analogy is, therefore, that light has
momentum p = h/. Therefore, matter waves are described by a wavelength

 = h/p = h/mv.

We can also express the kinetic energy of a particle in terms of this wavelength:

2
1 p2 1 h h2
E  mv 2      .
2 2m 2m    2m 2

As an aside, recall the equipartition principle. Then, we have that the kinetic energy for a
gas of particles (electrons, neutrons, etc.) = 3RT/2NA. So, we can equate the deBroglie
wavelength with the temperature of the gas of particles.

Problem: Calculate the speed (in m/sec) and kinetic energy (in eV) of an electron with a
wavelength  = 1.54 Å. Mass of the electron is 9.11  1031 kg; 1 eV = 1.609  1019 J.

h 6.63  1034 J  sec

v   4.73 106 m/sec = 0.0158 c
m  9.1110 kg 1.54 10 m 
31 10

 6.63  1034 J  sec 

2
h2
E   1.02 1017 J = 63 eV
2m 2 2  9.111031 kg 1.54 1010 m 2

This wavelength corresponds to X-radiation from Cu and is used for X-ray diffraction
experiments on solids. An electron microscope capable of TEM and electron diffraction
accelerates the incident electron beam toward the sample with speeds that reach ca. 1-2 %
of the speed of light.

(2) Bohr Model of the Atom

Another major problem facing physicists around the beginning of the 1900’s was to
explain the discrete lines observed when atomic gases emitted electromagnetic radiation
after being charged. This was first “explained” by Niels Bohr, whose model was later
shown to be false, but absolutely correct for only the hydrogen atom and atomic ions with
a single electron, e.g., He+, Li2+.

v
-
r

n=1

n=2

n=3

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In the Bohr model, the atom consists of a central nucleus with protons and neutrons and
the electrons move in specific orbits around the nucleus given an integer label (n), each of
which can be described by a distance from the nucleus (rn). Each orbit also has a specific
energy associated with it (En: energy is the sum of kinetic and potential energy; since the
electron is attracted to the nucleus, the energy of each orbit is a negative number, relative
to an isolated nucleus and an isolated electron). In this model, e.g., the H atom, there is a
single (massive) proton in the nucleus, charge +e, which remains stationary – no kinetic
energy. The electron, mass m, charge e, move in discrete orbits with radius r. To move
in these orbits, there are three conditions:

(1) The attractive force between the proton and electron = centripetal force causing the
electron to move away from the proton;
(2) Angular momentum (the momentum for a body to change direction) is quantized
into nh/2. (h has units of angular momentum (Jsec), n is a positive integer, and
2 in radians is 360 for a complete revolution of an electron about the proton in its
orbit);
(3) The energy of the electron = Kinetic Energy (mv2/2) + Potential Energy (e2/r).

The goal, therefore, is to determine the radii (r) and energies (E) of the allowed “orbits”
of the electron in this atom, written in terms of the fundamental constants, h, m, and e.

Derivation of Radius and Energy for the Bohr Atom:

mv 2 e 2
From (1): Centripetal Force = Electrostatic Force,  2.
r r
nh
From (2): Angular momentum = mvr  , n = 1, 2, 3, …
2
v
- 1 2 e2
r From (3): E  mv  .
2 r
+
Solving for r and E in terms of fundamental constants, h, m, and e:
n=1

 h2 
rn   2 2  n 2   0.529 Å  n 2 , n = 1, 2, 3, ...
 4 me 
n=2

n=3
 2 2 me 4   1   1 
  2     2.18  10 J   2 
18
En    2
 h  n  n 
 1 
  13.6 eV   2  , n  1,2,3,
n 

Therefore, Bohr showed that the electronic “orbits” and their energies are quantized. In
these expressions, 2.18  10–18 J = 13.6 eV is called the Rydberg; and 5.29  10–11 m =
0.529 Å is called the Bohr radius. The energies are negative (< 0), which means that the
electron is bound to the proton – the energy of the proton and electron held together is
lower than the energy when they are completely separated.

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The Bohr model is exact for atoms or ions with just one electron, i.e., H, He+, Li2+,…,
Fe25+,… For ions with Z protons, the expressions are

 Z2   Z2 
En    2.18  1018 J   2    13.6 eV   2  , n  1, 2,3,
n  n 
 n2   n2 
rn   0.529  1010 m      0.529 Å    , n  1, 2,3,
Z  Z 

The orbit with n = 1 is the lowest energy orbit that the electron can have; this situation is
called the ground state. For all other (higher) values of n, the electron would be in an
excited state. In atomic emission, the H atoms are exposed to high temperatures or
voltages, which put each H atom into an excited state (n > 1). The H atom, however, is
most stable when it exists in its ground state, so the atom releases light as the electron
drops into an orbit closer to the nucleus.

 h
We measure energy transitions between states: H(initial state)  H(final state)

0
En (eV) n=5 n=6
n=4
-2 n=3
"Emission"
n=2
-4

-6

-8

"Absorption"
-10

-12

n = 1 (Ground State)
-14
Absorption is the process in which an atom absorbs electromagnetic radiation and
changes from a state of low energy to a state of higher energy. Therefore, E > 0 and
nFINAL> nINITIAL. Emission is the reverse process: an atom releases light as it changes
from a state of high energy to a state of lower energy: E < 0, with nFINAL < nINITIAL. For
absorption to occur, light of specific wavelengths (frequencies) will be absorbed; likewise
for emission, light of specific wavelengths will be emitted. For any process,

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Unit #3 (Chemical Structure) 3-7

 1 1  hc
E  EnFINAL  EnINITIAL    2.18  1018 J   2  2  ; E  h  .
 nFINAL nINITIAL  
In this expression, E gives the energy change of the process; the magnitude of this
energy change (always positive) will give the frequency and wavelength of light for the
transition. The sign of E tells us whether the process is absorption (+) or emission ().

Problem: Calculate the wavelength (in nm) of light necessary to excite a hydrogen atom
from its ground state to the n = 4 state.

 1 1 hc
E  E4  E1    2.18  1018 J   2  2   2.044  1018 J 
4 1  
25
hc 1.99  10 J  m 10 nm 9
    97.3 nm
E 2.044  1018 J 1m

The Bohr model, although successful for the hydrogen atom, could not be refined to
account for the emission spectra of atoms with more than one electron. It turned out that
Bohr’s model was an ingenious oversimplification and was not really a fundamental
description of electronic states in atoms. In fact, Bohr’s model does not take into account
the wave nature of the electron. An important and fundamental outcome of this
characteristic is the Heisenberg Uncertainty Principle, which states that it is not possible
to determine simultaneously the position and the momentum of a particle with complete
exactness, i.e., without some error. It is expressed mathematically as xp  h, where x
is the error in position, p is the error in momentum. Therefore, a more fundamental
theory is needed, which uses the wave-particle duality of electrons.

A Digression: Exact Solution of a Simple but Pedagogically Useful Problem, the

Particle-in-the-Box

Before we begin the discussion of the quantum mechanical solution of the hydrogen
atom, whose details we can only outline, it is useful to work through the solution of a
simple but extraordinarily useful problem in quantum mechanics, referred to as the
particle-in-the-box.

Because particles exhibit wave-like behavior, it is necessary to have a wave equation for
particles, just as we have equations for electromagnetic waves, as you may have learned
in a physics course. A postulate of quantum mechanics is that there is such a wave
equation and that it has the following form.

 
 
           V ( x, y, z )   ( x, y, z )  E  ( x, y, z ).
2 2 2 2
 2 m  x 2 y 2 z 2   
    Potential Energy 
 inetic Energy 

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Unit #3 (Chemical Structure) 3-8

h
In this expression, the term in [ ]’s is called an operator, and  = .
2π
This equation is called the Schrödinger equation. Although it may seem very complicated, there
is a very simple application of it to a problem that is extremely useful and instructive. The
problem is called the one-dimensional particle-in-the-box. It treats a particle (any particle) that is
constrained to move in a box in one dimension, to which we refer here arbitrarily as the x
dimension, where 0 ≤ x ≤ L, and where L is the length of the box. The potential energy, V(x),
is zero inside the box; but at the edges, it rises infinitely rapidly to infinity: V(x) = 0 for 0 ≤ x ≤
L; V(x) = ∞ everywhere else.

The Schrödinger equation now has the greatly simplified form:

2 d 2
  ( x)  E  ( x).
2 m dx 2

Kinetic Energy

The constraints imposed by the potential walls dictate that the particle can only exist inside of the
box and that inside of the box all of its energy is kinetic energy. Also, because the particle is
moving in only one dimension, the wavefunction is only a function of x and the partial derivative
notation changes to a total derivative notation.

We are now in a position to solve this equation. First, it is useful to recall that the kinetic energy
is KE = ½mv2, where m and v are the mass and velocity of the particle. It is often more useful to
write the kinetic energy in terms of the particle’s momentum, p = mv, in which case
p2
KE =
2m
Above, we stated that the momentum of a particle is related to its wavelength by de Broglie’s
relationship
h 2π h
p = = k , where k = and  = .
λ λ 2π

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Unit #3 (Chemical Structure) 3-9

(“Broglie” is commonly mispronounced, even by the French. It rhymes exactly with the French
word “feuille,” and may be approximated in English by “broy.”). Making these substitutions, we
have
k 2 2
KE =
2m

and the Schrödinger equation can be rewritten as:

d 2 2m E
2
 
2
   k 2
dx 

This equation says that a nontrivial solution (i.e., a solution to the equation where ψ(x) is not
everywhere zero) must be a function that when differentiated twice gives itself back times a
constant. You can convince yourself that there are only three possible kinds of solutions to this
equation (linear combinations of these solutions are also solutions):
 A sin (kx)

ψ(x) =  B cos (kx) , where A, B, C, and k are constants.
 (ikx)
C e

(The k in the argument of the sine, cosine, and exponential functions is necessary because the
arguments of these functions must be unitless. The “argument” is the quantity enclosed in
parentheses for illustrative purposes. The parentheses are often omitted. Since x has units of
length, it is appropriate that it be multiplied by k, which has units of inverse length.)

In order to decide which of the three solutions is appropriate, we must consider the physics of the
problem, which is exactly analogous to the classical problem in optics of describing light between
two perfectly reflecting mirrors. The presence of the infinitely steep potential walls requires that
the particle cannot be found in the wall, and hence that its wavefunction go to zero at x = and x =
L. The sine function is the only one of the three functions that is zero when x = 0. We shall not
discuss the exponential here, but we do note that

eikx = coskx + i sin x

and hence that
eikx – e–ikx = 2i sinkx

In order for the sine function to be zero at x = L and thus satisfy the “boundary condition,” we
require that kL = nπ. This simple result, stemming from basic trigonometry, is fundamental to
understanding quantum mechanics. Because only sine functions, whose arguments kL = nπ
where n is a positive integer, obey the boundary conditions; and because k is related to the
momentum of the particle and consequently to its energy, the energy of the particle is quantized—
i.e., it can only exist in certain specified energy levels determined by k and the quantum number,
n.

It is important to appreciate that this is a result arising naturally from the properties that we
require of the wavefunction in solving the Schrödinger equation. (As discussed earlier, Bohr
knew that a similar result must be true for the hydrogen atom, namely that mvr = n. But he was

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Unit #3 (Chemical Structure) 3-10

unable to show why this must be true because he did not know the Schrödinger equation for the
hydrogen atom.) The energy levels for the particle in the box are thus given by:

k 2 2 n2 h2
En = =
2m
8mL2

The important results are that the spacings between energy levels:

1. increase quadratically with the quantum number, n.

2. are inversely proportional to the mass of the particle.
3. are inversely proportional to the square of the length of the box.

These latter two points explain why we see quantized energies of an electron in a box whose
length is on the order of several picometers but not for a golf ball in a shoebox, for example. The
ultimate reason for this deals with the magnitude of Planck’s constant. Roughly speaking,
quantum effects will be observed when
h2
~1
mL2

For any macroscopic system, e.g., the golf ball in the shoebox
h2
<< 1
mL2

and the spacings between the energy levels are negligibly small.

Why is it not possible to have n = 0? This is, after all, a perfectly acceptable mathematical
solution to our problem and satisfies the boundary conditions. The reason is that if we knew the
particle had n = 0, we would know that it had zero (kinetic) energy and hence zero momentum.
We could thus know its energy and position simultaneously and with perfect accuracy. This
violates a fundamental principle of quantum mechanics enunciated by Heisenberg. (If n ≥ 1, we
can know the absolute value of the particle’s momentum exactly, but we could not know whether
the particle is moving to the right or the left in the box.)

Finally we comment on the coefficient, A, of the sine function. Once we admit that particles have
a wavelike nature, we can no longer hope to speak about where these are with absolute certitude.
We can only talk about the probability of finding the particle somewhere in space. It is a
postulate of quantum mechanics to interpret the wavefunction, (x), in terms of this probability:
P(x)dx = probability of finding the particle between x and x + dx; and P(x)dx = (x) *(x)dx,
where * denotes complex conjugate of the function. In the case of the sine, which is real, the *
does not play a role and we have P(x) = A2sin2kx. The value of A is then obtained by realizing
that any probability distribution must satisfy the equation (see the discussion in Unit 1 regarding
probability distributions):
+
 P(x)dx = 1
-
In the case of the particle-in-the-box, since the particle can only be between x = 0 and x = L, we
have

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Unit #3 (Chemical Structure) 3-11

+ L
2 2 L
 P(x)dx = A  sin kx dx = A2 = 1
2
- 0

1/ 2 1/ 2
2
ψ n(x) =  L 
2 nπ x
and so A =   and sin .
L L

Two Examples of Applying the Particle-in-the-Box to Real Problems

A very common example of the rapidly growing field of nanotechnology is provided by

generating a set of particles of CdSe of uniform size, from 1 to about 10 nm, or so, as illustrated
in the photograph below, which has been taken from the general chemistry text by Brown et al.,
and annotated. Although the particles are not one-dimensional boxes, the same basic principles
are in effect. The smaller the particle, the larger the energy gap for a transition, and hence a
shorter wavelength of light is emitted. And the larger the particle, the smaller the energy gap for
a transition, and hence a longer wavelength of light is emitted.

Another example that we shall encounter later on in this unit (and in a problem at its end
involving hexatriene) is that of “conjugated polyenes,” molecules with alternating double bonds.
The bonding structure of these molecules provides a “box” along which electrons can move
freely. The length of the box determines the wavelengths that the molecules can absorb; and this,
in turn, determines the color of the substance. Dyes are molecules that have alternating double
bonds.

(3) Orbitals and Quantum Numbers for One-Electron Atoms and Ions

As indicated above, the wave-particle controversy for describing the electron in atoms caused
Bohr’s “particle-based” model to be abandoned in place of a so-called wave equation, called the
Schrödinger equation – i.e., quantum mechanics was developed. One representation of this
equation is a differential equation, the solutions of which give the possible states of the electrons,
which include the distribution in space of the electrons, described by a wavefunction (), and

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Unit #3 (Chemical Structure) 3-12

corresponding energies (energy E = kinetic + potential energy). The Schrödinger equation for a
one-electron, hydrogen-like atom or ion has the same form as the one we saw above:

 
 
           V ( x, y, z )  
2 2 2 2
( x, y, z )  En  n,l , m ( x, y, z ).
 2 m  x 2 y 2
z 2    n,l , m
    Potential Energy 
 inetic Energy 

As before, as with the particle-in-the-box, the term in [ ]’s is called an operator; and the first term
gives the kinetic energy and the second term gives the potential energy for an electron in the state
described by the wavefunction, n,l,m(x,y,z) and quantized energy En (NOTE: the energy for one
electron depends solely on one of the quantum numbers). The subscripts, n, l, and m are now
required because this problem is more complicated than that of the particle-in-the-box. We now
have an electron and a nucleus to consider, and these quantum numbers treat this complexity.

The wavefunctions in this problem are called orbitals because they resemble the orbits present in
the Bohr model. The word “orbital” is somewhat unfortunate because it can give the mistaken
impression that electrons are miniature golf balls that really orbit the nucleus in race tracks of
particular shapes. It must always be kept in mind that in this description, the electron is a wave.
Hence, care has been taken to italicize the word “resemble” in the paragraph above.

In an atom or ion with one electron, the potential energy is just the electrostatic attraction
between the nucleus and the electron. Solving the corresponding differential equation for the
energies gives the same result as from the Bohr model:

 1
En   13.6 eV   2  , n  1, 2,3,
n 

n,l,.m(x,y,z) = wavefunction for the electron, and are called atomic orbitals. Atomic
orbitals provide a description of how the electron is distributed in 3D space in the atom.
Now, the atom has spherical symmetry – the central nucleus is massive and considered
stationary, while the much lighter electron moves around the nucleus and smears out a
spherical shape. The expression for the Schrödinger equation (above) used Cartesian
coordinates, which do not conform exactly to the spherical symmetry. It helps
immensely to transform from Cartesian coordinates to spherical coordinates.

z z
(x, y, z) The ATOM has (r, , )
SPHERICAL
SYMMETRY 
r

y  y
x x
CARTESIAN Coordinates SPHERICAL Coordinates

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-13

The three spherical coordinates are (1) r = distance between the nucleus and the electron;
(2)  = angle between the z-axis and the radius line to the electron; and (3)  = angle
between the x-axis and the projection of the radius line into the xy-plane. When we
transform to this coordinate system, the Schrödinger equation is

 
 
    d  2 d  l  l  1 h   e  
2 2 2 2

 2m  dr 2 r dr 8 mr 2  r  n ,l ,m  r , ,    En  n ,l , m  r ,  ,   .

   Potential  
 Kinetic Energy
Energy 


In this equation, the potential energy operator contains the electrostatic attraction
between the proton in the nucleus and the electron. In the kinetic energy operator, we
find a term due to angular momentum (centripetal force), so this equation contains the
same physical effects used in the Bohr model. The solutions of the energy are exactly the
same as above; the wavefunctions (atomic orbitals) can now be written in a very
convenient form:

 n ,l ,m  r ,  ,    Rn ,l  r  Yl ,m  ,   .

Rn,l(r) is called the radial wavefunction, depends solely on r, the distance to the nucleus,
and is specified by quantum numbers n and l. Yl,m(, ) is called a spherical harmonic
wavefunction, depends solely on the two angles, and is specified by quantum numbers, l
and m. For an atomic orbital, Rn,l(r) specifies the shell, and Yl,m(, ) specifies the shape
and orientation of the orbital in space.

Boundary conditions restrict the behavior of the wavefunction and orbitals – in an atom,
the value of the wavefunction goes to “0” as the coordinates get infinitely far away from
the nucleus at the origin. There are three important boundary conditions with these
spherical coordinates:

(1)  n ,l ,m  r,  ,    0 as r  : as the position gets infinitely large, the value of the

atomic orbital must go to 0.
(2)  n ,l ,m  r,    ,     n ,l ,m  r,  ,   : it doesn’t matter how we orient the coordinate
system in space, but we do specify a unique axis (the z-axis).
(3)  n ,l ,m  r ,  ,   2    n ,l ,m  r,  ,   : the coordinate  can only be a single circle.

These boundary conditions create quantum numbers, there is one quantum number for
each “degree of freedom” of motion (dimension) – so, there are 3 quantum numbers: n, l,
m. Also, there is an infinite number of solutions – one of these gives the ground state, the
others give excited states for the electron.

Each atomic orbital is characterized by three quantum numbers:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-14

n: 1, 2, 3, 4, ...; principal quantum number, determines the energy of the orbital, and
labels a shell.

l: for a given n, l takes all values 0, 1, 2, ..., n  1; angular momentum quantum number,
describes the shape of orbitals. For l equal 0 = s orbital; 1 = p orbitals; 2 = d orbitals,
3 = f orbitals, called subshells.

m: for a given l, m takes all values –l, –l + 1, ..., l – 1, l; magnetic quantum number,
describes the orientation of the orbital with respect to a coordinate system. For each
subshell, l, there are 2l + 1 magnetic quantum numbers.

The solution of Schrödinger’s wave equation also gives quantized energy levels, En, that
depend only on the principal quantum number, n. The result is the same as the Bohr
result:

En = (2.18  1018 J)(1/n2); n = 1, 2, 3, 4, …

and can be plotted accordingly…

En (eV)
l=0 l=1 l=2
0
n=4
-2 n=3
2s 2p m = 2 1 0 +1 +2
n=2
-4
m =1 0 +1
-6

-8

-10

-12
1s
n=1
-14
m=0

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-15

We can also construct the following table:

n l m Name No. of Orbitals n+l

1 0 0 1s 1 1
2 0 0 2s 1 2
1 –1, 0, +1 2p 3 3
3 0 0 3s 1 3
1 –1, 0, +1 3p 3 4
2 –2, –1, 0, +1, +2 3d 5 5
4 0 0 4s 1 4
1 –1, 0, +1 4p 3 5
2 –2, –1, 0, +1, +2 4d 5 6
3 –3, –2, –1, 0, +1, +2, +3 4f 7 7

For a given shell, n, there are n subshells, each labeled by a different azimuthal quantum
number, l. For each subshell, l, there are 2l + 1 atomic orbitals. Therefore, for a given
shell n, there are n2 atomic orbitals.

What are the significance and characteristics of the atomic orbitals? Let’s start by
looking at a series of s atomic orbitals:  n ,0,0  r,  ,    Rn ,0  r  Y0,0  ,    Rn ,0  r  . Since
l = 0 and m = 0, the spherical harmonic function Y0,0(, ) will just be a pure number, so
the function becomes essentially just the radial function. Therefore, consider the
following plots for the 1s, 2s, and 3s atomic orbitals:

1s 2s 3s
0.4 0.4
1.0 s s s
0.2
0.2
0.5
r
r 0.0
r 0.0
0.0

0.04 0.010
 
1.0 
 s  s  s

0.02 0.005
0.5

r r r
0.00 0.000
0.0

1.0 1.5
2 
2  2 
4r  s 4r  s
1.5
4r  s 1.0

1.0 0.5
0.5
0.5
r r
r 0.0
0.0
0.0

The top curves show the atomic orbitals from r = 0 to large r values. The 1s orbital starts at 1, and drops
steadily toward 0, as demanded by the boundary condition (1). The 2s orbital starts at ca. 0.35, drops and
hits 0 continues into negative values, and then approaches 0 from the negative end at large r. The 3s

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-16

orbital crosses 0 twice. Positions where wavefunctions = 0 are called nodes. These are important because
as the number of nodes in a wavefunction increases, the energy associated with that wavefunction also
increases. The wavefunction itself has no physical significance (because it can take + and  values; even
complex values in some cases). But,  2n ,l ,m  r , ,  corresponds to the probability distribution of locating
an electron in the orbital at the coordinates  r , ,  . A more meaningful function is 4 r 2  2n ,l ,m  r , ,  ,
which measures the probability of finding an electron in the orbital at a distance r from the nucleus (4r2
is the area of the sphere, radius r, so multiplying the area by 2 gives this value). The maximum in this
curve gives the most probable distance of finding an electron in that orbital; and the total area under this
curve will be one, which means that the electron must be somewhere in space.

Other ways of representing these orbitals could involve computer graphics or drawing them by hand. The
color scheme indicates different signs of the wavefunction (orange = + valued; blue =  valued).

+  +

+ +

1s 2s 3s

The following table summarizes diagrams and functional forms for the atomic orbitals for
n = 1, 2, 3, and 4 shells (these are mostly important for typical chemical systems; other
more exotic orbitals are useful for understanding the concepts behind the shapes of
atomic orbitals). You can access a decent program at http://www.orbitals.com/orb/, by
David Manthey. This program allows you to view a number of atomic orbitals and to
rotate them interactively on your computer screen. (The symbol α means “proportional
to.” Normalization constants are omitted from this table for simplicity.)

(n l m) Name Picture Functiona, b Nodesc

1s (1 0 0) 1s 1s  e  r 0

2s (2 0 0) 2s  2s   2  r  e r 2 1

2p (2 1 0) 2pz  2 pz  re  r 2 cos   ze  r 2 1

 2 px  re  r 2 sin  cos   xe  r 2
2p (2 1 1) 2px 1
2py  2 p y  re  r 2 sin  sin   ye  r 2

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-17

3s (3 0 0) 3s  3 s   27  18r  2r 2  e r 3 2

3p (3 1 0) 3pz  3 pz  r  6  r  e  r 3 cos   z  6  r  e  r 3 2

 3 px  r  6  r  e  r 3 sin  cos   x  6  r  e  r 3
3p (3 1 1) 3px 2
3py  3 p y  r  6  r  e  r 3 sin  sin   y  6  r  e  r 3

3d (3 2 0) 3dz2  3 d 2  r 2 e  r 3  3cos 2   1  z 2 e  r 3 2
z

 3d xz  r 2 e  r 3 sin  cos  cos   xze  r 3

3d (3 2 1) 3dxz 2
3dyz  3d yz  r 2 e  r 3 sin  cos  sin   yze  r 3

 3d 2  r 2 e  r 3 sin 2  cos 2   x 2  y 2  e r 3
3d (3 2 2) 3dx2y2 x  y2
2
3dxy  3d xy  r 2 e  r 3 sin 2  sin 2  xye r 3

4s (4 0 0) 4s  4 s  192  144r  24r 2  r 3  e r 4 3

4p (4 1 0) 4 pz  4 pz  r  80  20r  r 2  e  r 4 cos   z  80  20r  r 2  e  r 4 3

 4 px  r  80  20r  r 2  e  r 4 sin  cos   x  80  20r  r 2  e  r 4

4p (4 1 1) 4 px 3
4 py  4 p y  r  80  20r  r 2  e  r 4 sin  sin   y  80  20r  r 2  e  r 4

4d (4 2 0) 4dz2  4 d 2  r 2 12  r  e  r 4  3cos 2   1  z 2 12  r  e  r 4 3

z

 4 d xz  r 2 12  r  e  r 4 sin  cos  cos   xz 12  r  e  r 4

4d (4 2 1) 4dxz 3
4dyz  4 d yz  r 2 12  r  e  r 4 sin  cos  sin   yz 12  r  e  r 4

 4d 2  r 2 12  r  e  r 4 sin 2  cos 2   x 2  y 2  12  r  e  r 4

4d (4 2 2) 4dx2y2 x  y2
3
4dxy  4 d xy  r 2 12  r  e  r 4 sin 2  sin 2  xy 12  r  e  r 4

4f (4 3 0) 4fz3  4 f 3  r 3 e  r 4 cos   5cos 2   3  z 3 e  r 4 3

z

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-18

4 f  r 3 e  r 4 sin   5cos 2   1 cos   xz 2 e  r 4

4f (4 3 1) 4fxz2 xz 2
3
4fyz2 4 f  r 3 e  r 4 sin   5cos 2   1 sin   yz 2 e  r 4
yz 2

4 f  r 3 e  r 4 cos  sin  cos 2  z  x 2  y 2  e  r 4

4f (4 3 2) 4fz(x2y2) 
z x2  y 2  3
4fxyz  4 f xyz  r 3 e  r 4 cos  sin  sin 2  xyze  r 4

4 f  r 3 e  r 4 sin 3  cos   cos 2   3sin 2    x  x 2  3 y 2  e  r 4

4f (4 3 3) 4fx(x23y2) 
x x 2 3 y 2  3
4fy(3x2y2) 4 f r e 3 r 4
sin  sin   3cos   sin    y  3x  y  e
3 2 2 2 2 r 4


y 3 x2  y 2 
a h2
For the functions in this table, r in units of the Bohr radius, a0  = 0.529 Å.
4 2 me 2
b
x  r sin  cos  ; y  r sin  sin  ; z  r cos  .
c
Does not include the “node” at r  .

Another table showing alternative representations…

l=0 l=1 l=2

n=1
1s(r)

0 nodes

n=2
2s(r)

2p(r)

r r
Node

1 node
(spherical node)

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-19

1 node
(planar node)

n=3
3s(r)

3d(r)
3p(r)

r r r

y
y

x x

x y

2 nodes
(2 spherical nodes) z z

y
x

2 nodes
(1 spherical node;
1 planar node) 2 nodes
(2 planar or conical nodes)

Two important aspects of atomic orbitals are their nodes and lobes. Consider the 3 2p
atomic orbitals:

z LOBES z 1 NODE
z (along y) (yz-Plane)
LOBES
(along z)

1 NODE y
x
(xy-Plane) y
y
x
x
1 NODE
(xz-Plane) LOBES
(along x)

2pz 2py 2px

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-20

Nodes are surfaces where  n ,l ,m  r ,  ,    0 . For these orbitals, the nodes are simply
planes. The lobes are regions where the orbital takes a nonzero value (either positive or
negative). These 2p orbitals show their lobes pointing along the directions of the label.
Another set of examples come from the n = 3 shell: the 3p atomic orbitals (illustrated by
just the 3pz orbital) and two of the 3d atomic orbitals (the 3dz2 and 3dyz orbitals):

z z
z

y
y x
y x
x

3pz 3dz2 3dyz

z
2 Conical
Spherical Node Nodes
y
 = 54.74
Planar Node  = 125.26 2 Planar
(xy-plane) Nodes
y
z (xz-plane)
x

From the previous two tables, we see that the 2p orbitals have 1 node (a plane), and the
3p/3d orbitals have 2 nodes. Furthermore, there are 3 different kinds of nodes: (a)
spherical nodes (r = constant); (b) conical nodes ( = constant; if  = 90); (c) planar
nodes ( = constant; these planes are parallel with the z-axis). In general, the quantum
numbers n, l, and m are node counters:

|m| = # of planar nodes;

l  |m| = # of conical nodes; therefore, l = # of conical nodes + # of planar nodes;
n  l  1 = # of spherical nodes (we are not counting the node as r  ).

Orbital Size: In the Bohr model, each orbit has a specific energy En and radius rn. The
wave-particle dual nature of the electron prohibits a specific localization of electron and
electronic wavefunctions in space, but we can identify the most probable distance for an
electron from the nucleus, depending upon the atomic orbital wavefunction. In the one-

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-21

electron Schrödinger equation for the H atom, the most probable rn is related to n2, but rn
 n2a0 (a0 = 0.529 Å). Here is a graph of the ns atomic orbital distributions for n = 1, 2,
3, and 4: at the very least, the most probable distance does increase with the value of n.

2
1s
4 Rns(r)

2s
3s
4s

(4) One-Electron Atoms and Ions

The only neutral atom that contains one electron is the hydrogen atom. Ions containing
just one electron include He+, Li2+, Be3+, …, Ca19+, etc. The allowed energy states for
this electron are given by the solutions (“atomic orbitals”) to the Schrödinger equation
presented in the previous section. The lowest energy state, called the ground state, of the
one-electron atom or ion occurs when the electron “occupies” this state, which is the 1s
atomic orbital.

Electron Spin: An electron has an intrinsic characteristic called spin, but this feature has
no classical origin; it is entirely a quantum mechanical phenomenon. Electron spin is
identified by a quantum number (s = 1/2), and it takes two possible values, ms = +1/2
(“spin up”) or 1/2 (“spin down”). We can see the effect of spin by exposing matter to a
magnetic field, but we can only see the effect of the sum of spins of all electrons in the
substance being examined. Here is a way that spin is represented on an orbital energy
diagram:

(n,l,m) (n,l,m)
SPIN UP SPIN DOWN

For a one-electron atom or ion, the state of the electron will be completely described by
four quantum numbers, (n, l, m, ms): three that identify the atomic orbital (n, l, m) and
one that identifies the spin (ms). With the two possible electron spin quantum numbers
(ms = +1/2, –1/2), each orbital gives rise to two distinct states, (n, l, m, +1/2) or (n, l, m, –
1/2). Since electrons are fermions, when we consider atoms or ions with more than one

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-22

electron, it turns out that an orbital can hold up to two electrons, one “spin-up,” and the
other, “spin-down.” (This is called the Pauli Exclusion Principle.)

How can we observe spin? We need to put the system into a magnetic field (a magnet).
The magnetic field will affect the energies of “spin up” and “spin down” differently.
Below is a diagram of the effect on an orbital that contains either one electron (left; “spin
up” only) or two electrons (right; “spin up” and “spin down”):

ENERGY MAGNETIC ENERGY MAGNETIC

FIELD FIELD

(n,l,m)
ms =

(Unpaired Electrons attracted to Magnet) (Paired Electrons not attracted to Magnet)

Both pictures show a single atomic orbital: the magnetic field splits the energy of the
“spin up” and “spin down” functions. If an orbital contains just a single electron, the
energy of the system goes down when placed in the magnet – it is attracted to the magnet
(paramagnetic). If an orbital contains two electrons, there is no energy change of the
system – it is not attracted to the magnet (diamagnetic).

(5) Multi-Electron Atoms/Ions

In multi-electron atoms (He, Li, …), the Schrödinger wave equation now involves the
kinetic energies and potential energies of all electrons. This potential energy includes the
attraction between each electron and the Z protons (atomic number) in the nucleus as well
as the repulsion between each pair of electrons. As an example, here is the Schrödinger
wave equation written out for the He atom (Z = 2):
 
 
 h 2  d 2 2 d l1  l1  1 h 2 d l2  l2  1 h  Ze 2 Ze 2
2 2
d2 e2 
  2  2    2       n ,l , m ; n ,l , m  r1 , 1 , 1 ; r2 ,  2 ,  2 
8 m  dr1 r1 dr1
  8 mr12 dr2 r2 dr2 8 mr22  r1 r2 r2  r1  1 1 1 2 2 2
    

 Kinetic Energy Potential 
 Energy 
 En1 ,l1 ; n2 ,l2  n1 ,l1 , m1 ; n2 ,l2 , m2  r1 , 1 , 1 ; r2 ,  2 ,  2 

In this complicated expression, the wavefunction uses coordinates for each electron; the
energies depend on the principle and azimuthal quantum numbers of both electrons. The
term in the equation that makes this problem very difficult to solve is the electrostatic
repulsion between the electrons (the last term in brackets). In fact, the wave equation
cannot be solved exactly – it can only be done by approximations and computations. For
these problems, the electronic wavefunctions are called multi-electron wavefunctions and
can be approximated as a product of atomic orbitals – these products are called electronic
configurations.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-23

Energies: In multi-electron atoms, the atomic orbital energies depend on the quantum
numbers n and l, but not on m. Therefore, the five 3d atomic orbitals all have the same
energy in an atom; the three 2p atomic orbitals all have the same energy. However, there
is no simple, general formula for energy in terms of n and l (as in the Bohr model or as in
the one-electron problem above). Nevertheless, there are two general guidelines that
allow quick determination of the ground state electronic configuration, specifically for
neutral atoms, i.e., the number of protons = the number of electrons:

(1) Atomic orbital energies tend to increase as n + l increases;

(2) If two subshells have the same n + l value, for example 3p and 4s, then the subshell
with the lower n value has the lower energy.

According to this recipe, the energies of the atomic orbitals would increase as follows:

Orbitals: 1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s …

n: 1 2 2 3 3 4 3 4 5 4 5 6
l: 0 0 1 0 1 0 2 1 0 2 1 0

(n + l): 1 2 3 3 4 4 5 5 5 6 6 6

The energy values of the different atomic orbitals can be plotted on an energy scale:

En,l 5p 5d
5s 4d
4p
4s 3p
3s 3d
2p
2s

1s

NOTE: This guideline is known as the “(n + l) rule,” and has been criticized. It is
important to realize at this point that the two guidelines above are tendencies, and the
most exceptions occur for guideline #1. In fact, there are 20 exceptions to the ground
state electronic configuration expected by these atomic orbital energies, in order of
increasing atomic number: they are Cr, Cu, Nb, Mo, Ru, Rh, Pd, Ag, Ce, Gd, Tb, Pt, Au,

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-24

Ac, Th, Pa, U, Np, Cm, and Bk, which means a slightly less than 20% success rate for
this model.

In the energy diagram above, you will see that the atomic orbital energies get
energetically closer together as the principal quantum number n increases; this behavior
is just like the atomic orbitals for the hydrogen atom. On this energy scale, we can
(perhaps) see that E(4s)  E(3d), E(5s)  E(4d), among others, which leads to the
exceptions mentioned above. In the next section, we will specifically address the cases of
Cr and Cu, which are both transition elements. For more details, see Journal of Chemical
Education, Vol. 73, pp. 498-503, 1996.

Wavefunctions: Although it is difficult to solve Schrödinger’s wave equation for multi-

electron atoms, we can still use the orbital concept – this is an approximation to the
actual (true) solution. In this model, we treat the electronic wavefunction as a function of
products of atomic orbitals. Each product is called an electronic configuration, and we
can symbolize a configuration by (n1l1m1)1(n2l2m2)1(n3l3m3)1. The configuration giving
the lowest energy of the atom is called the ground state (electronic) configuration. This
picture is the basis for the Periodic Table of the Elements as we know and use it, so that
leads us into the next section.

(6) Periodic Table of the Elements

The Periodic Table of the Elements is based on the relative atomic orbital energies
(shown above) as the number of electrons increases. The first period elements H and He
fill the 1s shell; the second period elements, Li-Ne, fill the 2s and 2p shell; and so on.
The successive placement of electrons in these atomic orbitals is referred to as the aufbau
principle, and gives the ground state electronic configuration, which is simply a listing of
the occupied atomic orbitals giving the lowest energy for the atom. It is best to learn
these by example:

Hydrogen (Z = 1) : (1s)1
Helium (Z = 2) : (1s)2
Lithium (Z = 3) : (1s)2(2s)1 = [He](2s)1
Carbon (Z = 6) : (1s)2(2s)2(2p)2 = [He](2s)2(2p)2
Oxygen (Z = 8) : (1s)2(2s)2(2p)4 = [He](2s)2(2p)4
Magnesium (Z = 12) : (1s)2(2s)2(2p)6(3s)2 = [Ne](3s)2

Writing out these configurations identifies different classifications of electrons and

atomic orbitals:

(a) Valence: highest value of n that contains electrons. Valence electrons are important
for chemical bonding with other atoms. Valence orbitals are the focus for chemistry;

(b) Core: all values of n below the valence level. Core electrons are important for
creating periodic behavior among the elements. The core electrons screen the

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-25

valence electrons from the nucleus, and, thus, are responsible for similar chemistry
among elements in the same group.

(c) Virtual: atomic orbitals that are unoccupied in the ground state of the atom. These
orbitals can be important for chemistry.

There are two primary rules to follow regarding allowable electronic configurations:

(1) The Pauli-Exclusion Principle, which states that, in an atom, no two electrons may
have the same set of four quantum numbers (n, l, m, ms). This means that for two
electrons to occupy the same atomic orbital, they must have opposite spins, i.e., one
with ms = +1/2, the other with ms = 1/2. For two electrons in different atomic
orbitals, they may have the same spin. Therefore, consider the He atom. For the
ground state of He, two electrons occupy the 2s orbital, and the two sets of quantum
numbers are:

1: (2, 0, 0, +1/2)
2: (2, 0, 0, 1/2), which is the only choice we have.

For an excited state of He, He*, with one electron in the 1s orbital and one in the 2s
orbital, we have the following possibilities:

1: (1, 0, 0, +1/2) 1: (1, 0, 0, +1/2) 1: (1, 0, 0, 1/2) 1: (1, 0, 0, 1/2)

2: (2, 0, 0, +1/2); 2: (2, 0, 0, 1/2); 2: (2, 0, 0, +1/2); 2: (2, 0, 0, 1/2)

These (four) different possible “microstates” contribute to the complexity of atomic

spectra (the emission of light from excited atoms).

(2) Hund’s Rule concerns how degenerate orbitals are filled to achieve the lowest energy
state. Degenerate orbitals are orbitals that have identical energies. So, the 2p
subshell contains three degenerate orbitals: m = 1, 0, +1 (or 2px, 2py, 2pz). Since
each orbital can accept two electrons, this subshell holds a maximum of 6 electrons.
Hund’s rules detail how the orbitals in this type of subshell are occupied if the
number of electrons is less than 6. For example, consider the oxygen atom. We have
an electronic configuration of (1s)2(2s)2(2p)4: the 2p subshell only has 4 electrons.
Hund’s rule states the electrons will occupy each degenerate orbital singly until all
orbitals have one electron each, and then any additional electrons must begin to fill
the orbitals. Thus, in the O atom, the first three electrons for the 2p subshell go into
the 1, 0, and +1 orbitals. The last electron can enter any one of these to complete
the electronic configuration. (The basis for this rule is Nature’s way to keep the
electron-electron electrostatic repulsion as low as possible.)

Using these rules and the atomic orbital energy scheme above, we can now account for
the Periodic Table of the Elements:

n s d (Transition Elements) p (Main Group)

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-26

1 H He
2 Li Be B C N O F Ne
3 Na Mg Al Si P S Cl Ar
4 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
5 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
6 Cs Ba Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
7 Fr Ra Lr Rf Db Sg Bh Hs Mt
f
(6) Lanthanides La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb
(7) Actinides Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No

Each period (row) in the Periodic Table corresponds to the valence shell of
orbitals/electrons. The groups identify the subshells that take the last remaining valence
electrons. For electron counting purposes, each orbital can hold 2 electrons. Since there
are 2l + 1 orbitals in each subshell l, each subshell contains a maximum of 4l + 2
electrons. Finally, since each shell n contains n subshells, it turns outs that there are n2
orbitals in each shell, and, therefore, a maximum of 2n2 electrons.

The orbital model is an approximation, though, to actual (true) solutions to Schrödinger’s

equation in multi-electron atoms. The problem is the electron-electron repulsion term:
electrons move with high speeds, and have most of the kinetic energy. If electrons did
not interact with each other, then the orbital picture would be just fine. Nevertheless, we
continue to use the orbital picture, because the solutions (energies and wavefunctions) are
very close to the orbital picture – the electron-electron repulsion is small compared to the
electron-nuclear attraction. Nevertheless, even the orbital model creates some subtle
effects: note that the atomic orbital energies get closer together as we go up in principal
quantum number. Now, consider the case of chromium (Z = 24):

Cr: expected electronic configuration = (1s)2(2s)2(2p)6(3s)2(3p)6(4s)2(3d)4

= [Ar] (4s)2(3d)4

but experimental measurements of atomic emission spectra indicate

Cr: observed electronic configuration = [Ar](4s)1(3d)5

[Ar](4s)2(3d)4 (4 unpaired electrons) [Ar](4s)1(3d)5 (6 unpaired electrons)

In the expected configuration, there are four unpaired electrons, whereas in the observed
configuration, there are six unpaired electrons. The observed situation would be the case
if the energies of the 4s and 3d atomic orbitals were nearly equal, because Hund’s rule
would abide – although the two sets of orbitals have different quantum numbers, they

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-27

would still be degenerate (having equal energies). This result implies that in Cr, E(4s) is
similar to E(3d).

For Cu, we can have the following scenarios:

Cu: expected electronic configuration = [Ar] (4s)2(3d)9

but experimental measurements of atomic emission spectra indicate

Cu: observed electronic configuration = [Ar](4s)1(3d)10

[Ar](4s)2(3d)9 (1 unpaired electron) [Ar](4s)1(3d)10 (1 unpaired electron)

Both configurations have the same number of unpaired electrons, so Hund’s rules do not
apply here. From the orbital model, we can therefore simply conclude that E(3d) < E(4s)
for Cu.

Therefore, these subtleties imply that the energy of the 4s and 3d atomic orbitals shift as
we move across the 4th period: to the left (K, Ca), E(3d) > E(4s); in the middle, E(3d) ~
E(4s); and to the right, E(3d) < E(4s). In fact, it is even more subtle than this simple
picture. We will address this subtlety later in this section.

(7) Lewis-Dot Structures

For chemists, the electronic configuration is a clumsy nomenclature to carry around, so

we use Lewis-dot structures for atoms and ions. These symbols are representations of the
atoms using just the electrons that are involved in holding the atom to other atoms in a
molecule or solid, i.e., electrons used for chemical bonding. They are important for main
group elements (s and p elements), but are usually not written for transition or rare-earth
elements (d and f elements). Take the O atom for example:

O: (1s)2(2s)2(2p)4 = [He](2s)2(2p)4

Only the electrons in the n = 2 shell are important for the chemistry and molecular
structures shown by oxygen. The two electrons in the 1s orbital are called core electrons;
the 1s orbital is called a core orbital. In the short-hand nomenclature above, this is
indicated by “[He]”, which shows the core. The six electrons in the n = 2 shell are called
valence electrons, because they are involved in connecting the oxygen atom to other
atoms by forming chemical bonds. The 2s and 2p orbitals are called valence orbitals.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-28

The Lewis-dot structure for an atom shows just the valence electrons, but it shows the
atoms as how they will form bonds (links) in molecules:

H He 1s

Li Be B C N O F Ne 2s, 2p

In the Lewis-dot structure, only the valence electrons are shown, next to the element’s
symbol. If electrons are paired (i.e., ms = +1/2 and 1/2), then they occur as a pair on the
same side of the symbol (right, left, top, bottom). For the second period elements, Li-C
show only unpaired electrons, while N-Ne show paired (and unpaired electrons).

Notice the difference between He and Be. He has the electronic configuration (1s)2,
while Be has the electronic configuration (1s)2(2s)2(2p)0. I have included the 2p subshell
in the description of Be because the energy difference between the 2s and 2p orbitals is
smaller than energies released when creating chemical bonds. Therefore, the Lewis-dot
structure represents the two valence electrons in Be as unpaired. Energy differences
between shells (different values of n) exceed bond energies; energy differences between
subshells (different values of l) generally do not exceed bond energies.

Example: What is the ground state electronic configuration of Sn (Z = 50)? How many
unpaired electrons are there? How many unpaired electrons are there in the Lewis dot
structure of Sn?

Sn belongs to the fifth period. The noble gas element at the end of the fourth period is
Kr, whose configuration is (1s)2(2s)2(2p)6(3s)2(3p)6(4s)2(3d)10(4p)6. Beyond these
orbitals, the electrons in Sn will fill the 5s and 4d subshells and then partially fill the
5p subshell. We can symbolize the core electrons as [Kr], and the ground state
electronic configuration of Sn is

[Kr](5s)2(4d)10(5p)2

In this configuration, there are two unpaired electrons, in the 5p subshell. The Lewis
dot structure, on the other hand, has four unpaired electrons, since Sn has four
electrons available for bonding.

Chemical Periodicity
READING: BLB-11, Ch. 7, 8.4; Probs: (7) 16, 26, 31, 44, 46, 61, 92; (8) 42, 97, 99
BLB-12, Ch. 7, 8.4; Probs: (7) 16, 26, 31, 44, 46, 61, 91, 101; (8) 44, 101, 103
PROBLEMS: 8

(1) Effective Nuclear Charge

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-29

The behavior of each chemical element depends on its valence electrons. The energies of
the orbitals occupied by the valence electrons are the highest among all occupied orbitals.
The core electrons and the core orbitals have much lower energies (more negative). The
reason for these differences is the concept of effective nuclear charge, which is a measure
of the net positive charge felt by a given electron in an atom or ion. Generally, the core
electrons feel a stronger attraction to the nucleus, and therefore a higher effective nuclear
charge than the valence electrons because the core electrons (negatively charged) screen
or shield the valence electrons from the nucleus. Consider, as an example, the Na atom
(Z = 11):

2 2
1s
4 R ns(r)
1
CORE 2s
3s
10 4s

11+

The Na atom has 11 protons in the nucleus; 10 core electrons and 1 valence electron. The
one valence electron does not feel the attraction of all 11 protons because the 10 core
electrons occur between the nucleus and the valence electron. On the other hand, the
wave-particle nature of electrons demands (and is seen in the graph of ns orbital
probability distributions) that the valence electron (in the 3s orbital) does penetrate near
the nucleus. Therefore, the valence electron will feel more than one positive charge (11
protons screened completely by 10 core electrons leaves 1+ net charge).

John Slater constructed some general (simple) rules for determining effective nuclear
charges (Zeff) for electrons in atoms:

Zeff = Z  S, where Z = atomic number (# protons in nucleus),

and S = “screening constant,” which depends on the distribution of es.

The screening constant for an electron is the sum of screening values for all other
electrons, i.e.,
N 1
S = S1 + S2 + S3 +  + SN  Si 
i 1
For these rules, we line up the subshells according to groups (in order of increasing n):

[1s] [2s 2p] [3s 3p] [3d] [4s 4p] [4d] [4f] [5s 5p] [5d] [5f] …
(Lower groups) (Higher groups)

Now, the rules depend on whether we are focusing on a s or p electron or a d or f

electron:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-30

A. For an electron in an [ns np] “group”:

(1) Each electron in higher groups: Si = 0;
(2) Other electrons in same group: Si = 0.35 (except 1s: Si = 0.30);
(3) Each electron in n  1 group(s): Si = 0.85;
(4) Each electron in n  2 or lower groups: Si = 1.00
B. For an electron in an [nd] or [nf] “group”:
(1) Rules A(1) and A(2) remain the same;
(2) Each electron in lower group: Si = 1.00

We can summarize these rules as follows:

(a) Core electrons shield valence electrons (nearly) completely;

(b) Valence electrons in the same subshell shield each other slightly;
(c) Within a single shell, s and p subshells shield d subshells, and so on.

Some example calculations:

Na (Z = 11): Electronic configuration = (1s)2(2s)2(2p)6(3s)1. Using Slater’s rules, what

are the effective nuclear charges for each of the subshells?

(1s): S = 1 (0.35) + 10 (0.00) = 0.35. Zeff = 11  0.35 = 10.65.

 (2s): S = 2 (0.85) + 6 (0.35) = 3.80. Zeff = 11  3.80 = 7.20.
 (2p): S = 2 (0.85) + 6 (0.35) = 3.80. Zeff = 11  3.80 = 7.20.
 (3s): S = 2 (1.00) + 8 (0.85) = 8.80. Zeff = 11  8.80 = 2.20.

Cu (Z = 29): Electronic configuration = [Ar](3d)10(4s)1. Using Slater’s rules, what are the
effective nuclear charges for the 3d and 4s electrons?

(3d): S = 18 (1.00) + 9 (0.35) = 21.15. Zeff = 29  21.15 = 7.85.

 (4s): S = 10 (1.00) + 18 (0.85) = 25.30. Zeff = 29  25.30 = 3.70.

NOTE: the higher effective nuclear charge for the 3d electrons agrees with the conclusion
that E(3d) < E(4s).

Now, consider the excited state configuration of Cu*: [Ar](3d)9(4s)2. What are the
corresponding effective nuclear charges?

(3d): S = 18 (1.00) + 8 (0.35) = 20.80. Zeff = 29  20.80 = 8.20.

 (4s): S = 10 (1.00) + 17 (0.85) + (0.35) = 24.80. Zeff = 29  24.80 = 4.20.

These values are both lower than the ones above, with Zeff for the 3d electron higher than
Zeff for the 4s electron. This again implies that E(3d) < E(4s).

It is important to understand how effective nuclear charges vary within the Periodic
Table, i.e., what are the trends across periods (rows) and down groups (columns):

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-31

Rows: Zeff increases from left-to-right – the number of core electrons remains
constant, while Z increases and the additional valence electrons do not screen each
other effectively.

Columns: Zeff remains nearly constant (very slightly increases) from top-to-bottom,
but the variation is much lower than within a single row.

Effective nuclear charge affects trends in atomic sizes, ionization potentials, electron
affinities, and, therefore, atomic orbital energies, which are of fundamental importance
for understanding how different elements will form chemical bonds.

(2) Periodic Trends

(a) Atomic and Ionic Sizes: We model atoms and monatomic ions as “hard” spheres.
BUT, the electronic wavefunctions do have nonzero on values as the function gets very
far away from the nucleus. Therefore, from the point of view of quantum mechanics,
atomic sizes have no real meaning. Nevertheless, there is a lot of data of interatomic
distances based on diffraction and spectroscopic experiments of solids and molecules,
and chemists do think about the sizes of atoms as a useful characteristic. Sizes are
identified by a radius of a sphere used to describe the atom or ion. There are many
various types of atomic radii.

Source: http://www.crystalmaker.com/support/tutorials/crystalmaker/atomicradii/

The following images are generated using CrystalMaker®, a crystal and molecular visualization program
for Mac and Windows, from CrystalMaker Software Ltd. (www.crystalmaker.com).

(i) Atomic radii: size of electrically neutral atoms, determined by interatomic distances
in the crystal structure of each element. Most metallic elements are close packed
(coordination number = 12); the nonmetallic elements have network structures.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-32

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(ii) Covalent (Bonded) radii: effective size of atoms when they chemically bond to
other atoms by sharing their valence electrons. This is determined by measuring
bond lengths between covalently bonded atoms (by X-ray diffraction or
spectroscopy). If the bond involves two identical atoms (Cl-Cl, F-F, N-N), then the
covalent radius is just one-half the bond distance.

Source:  2008 CrystalMaker Software Limited. All rights reserved worldwide.

For the transition metals, there is a slight contraction at the beginning of the series,
but then these metal atoms show similar sizes. The size is determined by the 4s
electrons. The pull of the increasing number of protons in the nucleus is more or
less offset by the extra screening due to the increasing number of 3d electrons.
Here is a schematic magnification of these covalent radii for the 3d elements.

(iii) Ionic (Crystal) radii: effective sizes of ions as determined by distances between ions
in salts. Cations give smaller radii than their parent atoms, anions give larger radii
than their parent atoms. Compare Na with Na+, Cl with Cl below.

An isoelectronic series is a group of ions that have the same number of electrons.
For example: O2, F, Na+, Mg2+, Al3+. Along this series, the ionic radius decreases
due to an increasing nuclear charge.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-33

In this table, the radius of the O2 ion is set at ca. 140 pm. This provides a reference
distance against which all other ions can be compared. This selection is completely
arbitrary, but is based on examination of a huge database of crystal structure data on
inorganic and organic salts. The alkali metals have charge +1, the alkaline earth
metals +2, the halogens 1. The radii of the transition metals depend on the charge,
which are commonly +2 or +3.

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(iv) van der Waals (Nonbonded) radii: effective size of an atom when it is not involved
in chemical bonding to another atom. These are determined from the contact
distances between non-covalently bonded atoms, but these atoms are probably near
each other, i.e., “touching.” These are determined from crystal structure and
spectroscopic data.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-34

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(v) Slater radii: sizes of atoms determined from a large database of crystal structures
empirically selected to optimize interatomic distances in crystals. For these radii,
we can predict distances between atoms in new solids: dAB = rA + rB.

Source:  2008 CrystalMaker Software Limited. All rights reserved worldwide.

Atomic/Ionic radii are frequently controversial, but the general trends are:

(1) Within each group (column), atomic radii increase from top-to-bottom due to an
increase in n; the number of core electrons increases.
(2) Within each period (row), atomic radii tend to decrease from left-to-right due to an
increasing effective nuclear charge, but there can be subtle effects that violate this
trend.

NOTE: atomic or ionic radii are completely unrealistic due to quantum mechanics, BUT
they are tremendously useful for anticipating distances between atoms or ions in
molecules and solids.

(b) Ionization Energies: energy required to remove electrons from gaseous atoms or
molecules. An interpretation of these energies is a measure of the orbital energy from
which the released electron originates:

H(g)  H+(g) + e H = I(H) = +1312 kJ/mol = +13.6 eV

NOTE: The energy of the 1s atomic orbital containing one electron (ground state
electronic configuration of H) is 13.6 eV relative to the proton and electron completely
separated from one another. Also, I > 0 because it takes energy to release an electron
from a neutral atom.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-35

For multi-electron species, these are called “first ionization energy (I1),” “second
ionization energy (I2),” and so on for successive removal of electrons. For a given atom,
ionization energies increase I1 < I2 < I3 < …

First ionization: Mg(g)  Mg+(g) + e H = I1(Mg) = +738 kJ/mol

Second ionization: Mg+(g)  Mg2+(g) + e H = I2(Mg) = +1451 kJ/mol
Third ionization: Mg2+(g)  Mg3+(g) + e H = I3(Mg) = +7733 kJ/mol

NOTE: Mg(g)  Mg2+(g) + 2e H = I1(Mg) + I2(Mg) = +2189 kJ/mol

Note the sharp increase in ionization energies from I2 to I3 (also, the significant difference
to remove the two valence electrons compared to the third electron from Mg) – the first
two electrons are removed from the valence 3s orbital, but the third electron must be
removed from the core 2p orbital, and costs much more energy.

kJ/mol
2500

s d p
2000

1500
n=1

1000 n=2
n=4
n=3
n=5
500

0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

Group
Trends in first ionization energies: tend to increase across a row, but we must look at the
electronic configurations of both the reactant and the product.

I1(Be) > I1(B): Be(g)  Be+(g) + e H = I1(Be) = +899 kJ/mol

[He](2s)2 [He](2s)1

B (g)  B+(g) + e H = I1(B) = +801 kJ/mol

[He](2s)2(2p)1 [He](2s)2

(B+ has an empty 2p subshell)

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-36

I1(N) > I1(O): N(g)  N+(g) + e H = I1(N) = +1402 kJ/mol

[He](2s)2(2p)3 [He](2s)2(2p)2

O (g)  O+(g) + e H = I1(O) = +1314 kJ/mol

2 4 2 3
[He](2s) (2p) [He](2s) (2p)

(O+ has a half-filled 2p subshell)

Electronic configurations of ions also follow the aufbau principle, with the general rule
that electrons are always removed from the highest shell (n). Examples:

S4+ (164 = 12 electrons; like Mg): [Ne](3s)2

Ti2+ (222 = 20 electrons; like Ca?): [Ar](4s)2 violates the rule; rather [Ar](3d)2.

NOTE: the energies of atomic orbitals depend significantly on the total numbers of
electrons. In the gaseous, neutral atoms, the energy of the 4s atomic orbital is close and
often lower than the energy of the 3d atomic orbital. When an atom loses electrons
(ionizes), the energy of the 3d orbitals drops quickly – these 3d electrons feel a higher
effective nuclear charge than the 4s electrons, so the 4s orbital loses its electrons first.

(c) Electron Affinities: energy required or released to add an electron to a gaseous atom
or molecule to form a negatively charged ion. For example,

H(g) + e  H(g) H = EA(H) = 73 kJ/mol = 0.76 eV

(13.6 eV) (14.36 eV or 7.18 eV/electron)

In this case, H(g) has a closed shell electronic configuration, (1s)2, but we have 1 proton
holding 2 electrons. Electron-electron repulsion keeps the electron affinity much less
than 13.6 eV, the energy of the atomic orbital in H(g).

Trends in electron affinities are not as apparent as for ionization energies. However, it is
again important to examine both the reactant and product electronic configurations.
Many EA < 0, but some that are > 0 include Be, Mg, N and the noble gas elements (He,
Ne, Ar, …).

F (g) + e  F(g) H = EA(F) = 328 kJ/mol

[He](2s)2(2p)5 [He](2s)2(2p)6

Ne (g) + e  Ne(g) H = EA(Ne) > 0 kJ/mol (unknown)

[He](2s)2(2p)6 [He](2s)2(2p)6(3s)1

One important trend occurs among the halogens: EA(F) = 328 kJ/mol; EA(Cl) = 349
kJ/mol; EA(Br) = 325 kJ/mol; EA(I) = 295 kJ/mol. All are negative due to closed shell
configuration of the negative ion. Along the group F-Cl-Br-I, the atoms get larger. So, in
F, there is a stronger electron-electron repulsion due to the small size; as the atoms get

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-37

larger, there is a weaker electron-nucleus attraction. So, trends are influenced by

electrostatic interactions.

(d) Electronegativities: Chemical concept, defined by Linus Pauling, and is not

measureable, but is based largely on chemical intuition. It is the “ability of an atom in a
molecule or solid to attract electrons to itself.” There are many quantitative scales of
electronegativity – the larger the value, the greater the electronegativity; the smaller the
value, the lower the electronegativity. Pauling’s scale goes from 0 to 4 (EN(F) = 4 is the
most electronegative element; EN(Cs) = 0.7 is the most electropositive element).

Table of Electronegativities (L. Pauling)

H He
2.20
Li Be B C N O F Ne
0.98 1.57 2.04 2.55 3.04 3.44 3.98
Na Mg Al Si P S Cl Ar
0.93 1.31 1.61 1.90 2.19 2.58 3.16
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
0.82 1.00 1.36 1.54 1.63 1.66 1.55 1.83 1.88 1.91 1.90 1.65 1.81 2.01 2.18 2.55 2.96 3.00
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
0.82 0.95 1.22 1.33 1.60 2.16 1.90 2.20 2.28 2.20 1.93 1.69 1.78 1.96 2.05 2.10 2.66 2.60
Cs Ba Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
0.79 0.89 1.27 1.30 1.50 2.36 1.990 2.20 2.20 2.28 2.54 2.00 1.62 2.33 2.02 2.00 2.20
Fr Ra Lr Rf Db Sg Bh Hs Mt Ds Rg Cn
0.70 0.90

La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb
1.10 1.12 1.13 1.14 1.13 1.17 1.20 1.20 1.10 1.33 1.23 1.24 1.25 1.10
Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No
1.10 1.30 1.30 1.38 1.36 1.28

One interpretation based on atomic properties (due to Robert Mulliken) is

EN = C(I1  EA); where C = constant to create a scale (= 0.002 to match Pauling’s scale)

H(g)  H+(g) + e(g) H = I1(H)

H(g)  H(g) + e(g) H = EA(H) = “I0” (ionization of the negative ion)

I: measure how much energy needed to remove an electron;

EA: measure how much energy gained to add an electron.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-38

In general, for a given element, a plot of ionization energies In vs. n (n = 0, 1, 2, …) can

be fit by the curve In = A + Bn + Cn2 (a parabolic function). For this fit, I0 = EA. For
example, see the graph of these values and the curve fit for sulfur:

Also, look at the following values:

F: I(F)  EA(F) = 2009 kJ/mol = 4.02
10000
In (kJ/mol)
8000
O: I(O)  EA(O) = 1455 kJ/mol = 2.91
2
6000 S: In = 218 + 711n + 115n

4000 Cl: I(Cl)  EA(Cl) = 1600 kJ/mol = 3.20

2000
S: I(S)  EA(S) = 1200 kJ/mol = 2.40

Li: I(Li)  EA(Li) = 580 kJ/mol = 1.16

0

0 1 2 3 4 5 6 Na: I(Na)  EA(Na) = 549 kJ/mol = 1.10

n

(e) Atomic Orbital Energies: AO energies tend to follow electronegativities, and this is
valuable for understanding the chemical behavior of elements in compounds, whether in
molecules or solids. Below is the trend in 1s, 2s and 2p atomic orbital energies for the
first and second periods. As the electronegativity increases (Li-Ne), both the 2s and 2p
atomic orbital energies decrease, with the 2s AO energy dropping faster, so that the
difference, E(2p)  E(2s), increases as electronegativity increases. The graph on the left
shows the first and second period elements on the same energy scale; the graph on the
right is a 10 magnification of the energy scale to emphasize the difference between 2s
and 2p atomic orbital energies.

H He Li Be B C N O F Ne H He Li Be B C N O F Ne

(eV) (eV) 0
0
2s
-100 2p -10

-200 -20

1s 2p
-300 -30

-400 -40 2s

-500 -50 1s

-600 -60

-700 -70

-800 -80

-900 -90

H He Li Be B C N O F Ne H He Li Be B C N O F Ne

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-39

Chemical Bonding in Molecules and Solids

READING: BLB-11, Ch. 8, 9, 11.8, 12.2 Probs: (8) 34, 46, 50, 54, 56, 81, 86;
(9) 21, 22, 24, 26, 36, 59, 60, 62, 66; (11) 72; (12) 12, 24
BLB-12, Ch. 8, 9, 12.4, 7 Probs: (8) 36, 48, 52, 56, 58, 67, 68, 87, 88;
(9) 27, 28, 29, 31, 44, 50, 51, 56, 71, 72, 74, 78, 83;
(12) 11, 66, 72, 74
PROBLEMS: 9-15

The basis for chemical bonding models in molecules and solids also relies on solving the
Schrödinger wave equation. For such structures, this is an extremely complicated problem, and
cannot be solved exactly because of the many particles making up a molecule, i.e., protons,
neutrons (in the nuclei) and electrons. To see how complicated the problem can be, even for a
very simple molecule, let’s look at the complete Schrödinger wave equation for the H2 molecule.
In this equation, we have H atom #1 (proton 1 + electron 1) and H atom #2 (proton 2 + electron
2); the masses of the protons are M, the coordinates are Ri = (Xi, Yi, Zi); the masses of the
electrons are m, the coordinates are ri = (xi, yi, zi).

 h2  d 2 d2 d2 d2 d2 d 2 
 2    2   2 
 8 M  dX 1 dY1 dZ1 dX 2 dY2 dZ 2  
2 2 2 2

 h2  d 2 d2 d2 d2 d2 d2  
 2  2  2  2  2  2  2  
 8 m  dx1 dy1 dz1 dx2 dy2 dz2  
   Q  r1 , r2 ; R1 , R 2   EQ  R1 , R 2   Q  r1 , r2 ; R1 , R 2 
 e2  e2 e2  
 R  R   r  R  r  R  
 2 1  1 1 2 2 

  e2 e 2
 e 2 
    
  r1  R 2 r2  R1  r1  r2 

The expression in [ ]’s is the kinetic energy + potential energy operator and includes terms for
the nuclei and the electrons. In order, they are: (i) kinetic energy of the nuclei; (ii) kinetic energy
of the electrons; (iii) repulsion between nuclei p1 and p2; (iv) attractions between electron and
proton within each atom (e1 and p1; e2 and p2); (v) attractions between electron and proton
between atoms (e1 and p2; e2 and p1); and (vi) repulsion between electrons e1 and e2. The
solutions to this equation are the wavefunctions, which are given with respect to the coordinates
of the electrons and protons, and the energies, which depend solely on the positions of the nuclei
(protons). There are quantum numbers {Q}, but these are no longer {n, l, m}.

To simplify this equation, we use the fact that the protons are 2000 more massive than the
electrons, so that the kinetic energies of the protons (speeds) are much smaller than those of the
electrons, and are considered to be zero, i.e., stationary nuclei at R1 and R2. This is called the
Born-Oppenheimer approximation. The new equation to solve now involves just the coordinates
of the electrons, while the coordinates of the nuclei are fixed.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-40

 h2  d 2 d2 d2 d2 d2 d2  
 2  2  2  2  2  2  2  
 8 m  dx1 dy1 dz1 dx2 dy2 dz2  
    Q  r1 , r2   EQ  R 2  R1   Q  r1 , r2 
  e
2
e2   e2 e2  e2 
 
    
  
  r1  R1 r2  R 2   r1  R 2 r2  R1  r1  r2 

This equation is typically solved for several different settings of the nuclear coordinates, R1 and
R2. In this way, the relationship between the energy and the structure (distance between the
nuclei) can be assessed. As with the Schrödinger wave equation for atoms, we will be interested
only in the solutions to this wave equation for molecules. Methods to solve this equation involve
computation. One code is GAMESS (http://www.msg.chem.iastate.edu/gamess/gamess.html),
which is written by Prof. Mark Gordon (ISU) and his group members.

(1) Molecular Orbitals

Just like atoms, the electronic structures of molecules and solids are described by
orbitals, but we can no longer use the same quantum numbers, because the geometrical
structure of molecules and solids is not the same as atoms. Nevertheless, electrons still
have spin, and electron configurations in molecules follow the same aufbau principle,
Pauli Exclusion Principle and Hund’s rules as in atoms. Molecules contain just a few
atoms, and their spectra have discrete energy levels. Solids contain 1023 atoms, and so
there are quasi-continuous bands of energy levels.

(a) Bonding and Antibonding Orbitals: For a simple idea of how two atoms interact to
give a molecule, consider the hydrogen molecule forming from two hydrogen atoms: 2 H
 H2. Here is a picture of how the potential energy changes with the distance between
the H atoms:

The reference energy is for the H atoms, each with an electronic

Energy
configuration of (1s)1. As the two H atoms come together, they feel an
He2(g)
attractive force, and their energy drops. At some point (0.75 Å), a
minimum is reached: if the H atoms come any closer, they repel each
Distance
0 other strongly. We symbolize the bond in H2 as HH.
H2(g)
On the other hand, there is no He2. Two He atoms repel each other
(see dashed line). The electronic configuration of each He atom is
(1s)2.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-41

(x)
a(x) b(x) In these molecules, we can describe the electronic structure by
bonding and antibonding orbitals: combinations of atomic orbitals by
x
either constructive (+, in phase) or destructive (, out of phase)
Ha Hb interference.
(x)

bonding(x) = a(x) + b(x) (Left) Two separate 1s atomic orbitals on separate H atoms, Ha and Hb.
Adding them gives a bonding molecular orbital – large values between
x nuclei. Subtracting them gives an antibonding molecular orbital – a
node occurs halfway between the nuclei.
(x) antibonding(x) = a(x)  b(x)

Energy s

Antibonding Molecular Orbital

Ha 1s Hb 1s

s

Bonding Molecular Orbital

The figure above shows a molecular orbital energy diagram for this process. Imagine
bringing two H atoms together, each with one electron in its 1s atomic orbital.
Constructive interference (adding) of the two atomic orbitals (AOs) creates a molecular
orbital (MO) with no node between the atoms – we can say that the wavelength
associated with the AOs increases when combined this way. Therefore, the energy of this
orbital goes down compared to the separated AOs – a bonding MO. Destructive
interference (subtracting) of the two AOs creates a MO with one node between the atoms
– its wavelength has decreased and its energy goes up – an antibonding MO. The Pauli
Exclusion Principle allows each MO to accept no more than 2 electrons (spin up and spin
down).

In H2, two electrons can fully occupy the bonding MO, and this represents a favorable
configuration compared to two separated H atoms. We can identify an index, called the
bond order:

Bond Order = [# e in bonding orbitals  # e in antibonding orbitals] / 2

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-42

In H2, this bond order is 1 – a single bond holds H atoms together.

In “He2,” there are four valence electrons. So. two electrons would occupy the bonding
MO and two electrons would occupy the antibonding MO. The bond order is 0 and there
is no driving force to bring two He atoms together to form a chemical bond.

(b) Electronegativity Effects: We can use this picture to describe three types of
interactions: (i) covalent bonds; (ii) polar covalent bonds; and (iii) ionic bonds. In purely
covalent bonds, the molecular orbitals are formed from atomic orbitals of the same
energy, e.g., HH, SiSi, etc. In purely ionic bonds, the filled bonding MO comes from
the lower energy AO; the empty antibonding MO comes from the higher energy AO.
What controls the energy of atomic orbitals? Two factors: (1) the energy lost when an
electron is removed from the orbital (ionization); and (2) the energy gained when an
electron is added to the orbital (electron affinity). These factors are combined in a
numerical scale of elements called electronegativity. In the periodic table, alkali and
alkaline earth metals have low electronegativities; halogens, oxygen and sulfur have high
electronegativities.

When forming bonding and antibonding MOs from AOs on different atoms, the
following rules apply:

(a) The more electronegative orbital has the greater contribution to the bonding MO;
(b) The less electronegative orbital has the greater contribution to the antibonding MO.

Covalent Bonding Polar-Covalent Bonding Ionic Bonding

AA A+B A+X
(H-H) (H-F) (Li-F)
“nonpolar bond” “polar bond” “ionic bond”
 = 2.1  2.1 = 0  = 4.0  2.1 = 1.9  = 4.0  0.9 = 3.1

Covalent Bonding: the electron pair is equally shared between the two atoms. The energy
difference between the bonding and antibonding MO depends on the strength of the
orbital overlap, which tends to increase as the distance between atoms decreases.

Ionic Bonding: the electropositive element completely gives its electron to the
electronegative element. The energy difference between bonding and antibonding MO
depends on the energy difference between the two AOs.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-43

Polar-Covalent Bonding: there is partial electron transfer and partial sharing of the
electron pair. This is the most common form of orbital interactions in molecules and
solids.

Using Pauling’s electronegativity scale (), a general rule of thumb is

(i) Nonpolar bond: if the electronegativity difference between atoms is less than 0.5;
(ii) Polar bond: if the electronegativity difference between atoms is more than 0.5 and
less than 2.0;
(iii) Ionic bond: if the electronegativity difference between atom is more than 2.0.

(c) Types of Orbital Overlap: Different AOs lead to different types of orbital overlap in
forming MOs. The different types of overlap, which label the type of chemical bonding,
differ by the number of nodal planes that contain the two atoms and the line between
them:


 There are no nodal planes containing the
 bond axis. There can be bonding and
 (sigma) antibonding overlap. (NOTE:  is Greek
“s”.) These figures show s-s, s-p and p-p 
overlap.

 There is one nodal plane containing the

 (pi) bond axis. (NOTE:  is Greek “p”.) -
overlap cannot involve s AOs, just p, d, …


 (delta) There are two nodal planes containing the
bond axis. (NOTE:  is Greek “d”.)

For creating molecular orbital (MO) energy diagrams, the following rules apply:

(1) The total number of MOs formed equals the number of AOs you start with;
(2) Only AOs with similar overlap characteristics can combine to form bonding and
antibonding pairs, i.e.,  overlap,  overlap or  overlap;
(3) The energy separation between bonding and antibonding MOs increases (generally)
according to the sequence:  overlap >  overlap >  overlap.

As a visualization of point (2), the following two situations give no overlap, and do not
constitute a valid combination of AOs via constructive (bonding) or destructive
(antibonding) interference:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-44

Point (3) is important for putting MO energy diagrams together, especially as we look at
Lewis structures:

ENERGY 






(d) Main Group Diatomic Molecules: an application of these ideas is found for the main
group (valence s and p) atom diatomic molecules, e.g., Li2-“Ne2.” To construct the
MO energy diagram, we start with the valence AOs of each element: one valence s
orbital and three valence p orbitals (px, py, pz). We can ignore the core orbitals – these
are tightly held to the nucleus and not involved in chemical bonding (significant
orbital overlap). Let’s consider the second period elements (Li-Ne). The valence
AOs are the 2s and 2p orbitals. We get the following MO energy diagram:

Energy *2p

*2p

2p 2p

2p

px py pz 2p

*2s

2s 2s

2s

This pattern of molecular orbitals relies on the energy difference between 2p and 2s AOs
to be large, as is seen for O, F, and Ne. For the earlier elements, B, C, and N, this energy

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-45

difference is smaller and has a profound influence on the pattern of molecular orbital
energies:

*p
*p

2p 2p 2p 2p
p
p

2s *s 2s

*s
2s 2s
s
s

When the E2pE2s gets smaller, there can be hybridization between valence s and p AOs.
The effect is that the energy of the p MO moves up in energy (through lower overlap
between atoms), but there is no relative change in the  MOs, so the following patterns
occur in diatomic molecules:
*2p *2p

*2p *2p

2p
2p

2p
2p

*2s *2s

2s 2s

Pattern of MOs for Pattern of MOs for

O2, F2 and “Ne2” B2, C2 and N2

The electronic configurations follow the aufbau principle, the Pauli Exclusion Principle
and Hund’s rules. When all electrons are paired in a chemical system (as in a filled
atomic orbital), then the system is called diamagnetic, which means it will be repelled by
magnet. If there are unpaired electrons in a chemical system (as in a partially filled
atomic orbital), then the system is called paramagnetic, and the system will be attracted to
a magnet. Most substances (molecules and solids) are diamagnetic, i.e., all electrons are
paired. Examples include H2, N2, chalk. Some substances are paramagnetic, e.g., iron,
O2. N2(l) is a colorless substance, which passes through the magnet poles. O2(l) is a blue

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-46

liquid, which is pinned between the magnet poles due to the presence of unpaired
electrons.

Electronic # Unpaired Magnetic Bond Bond Energy Bond

Configuration Electrons Behavior Order (kJ/mol) Length (Å)

Li2 (s)2 0 Diamagnetic 1 99 2.672

Be2 a (s)2(*s)2 0 Diamagnetic 0 ca. 10 2.449
2 2 2
B2 (s) (*s) (p) 2 Paramagnetic 1 347 1.589
C2 (s)2(*s)2(p)4 0 Diamagnetic 2 614 1.312
2 2 4 2
N2 (s) (*s) (p) (p) 0 Diamagnetic 3 941 1.094
O2 (s)2(*s)2(p)2(p)4(*p)2 2 Paramagnetic 2 495 1.207
F2 (s)2(*s)2(p)2(p)4(*p)4 0 Diamagnetic 1 155 1.435
b 2 2 2 4 4 2
Ne2 (s) (*s) (p) (p) (*p) (*p) 0 Diamagnetic 0 0.33 3.1
a
See Chemical Physics Letters, Vol. 109, Pp. 436, 1984 for report of the beryllium dimer.
b
See Chemical Physics Letters, Vol. 348, Pp. 67-74, 2001 for report of the neon dimer.

According to this model, we can now understand the magnetic response of N2 and O2.
We can also calculate the bond order for these diatomic molecules:

Bond Order = (# electrons in bonding MOs  # electrons in antibonding MOs) / 2

Take N2. There are 8 electrons in bonding MOs, 2 electrons in antibonding MOs. The
bond order is [(82)/2]/1 = 3 – we call this a “triple bond.” The bonds in O2 and C2 are
“double bonds,” the bonds in F2, B2 and Li2 are “single bonds.”

The bond order is useful because it correlates with trends in bond energies and often bond
lengths. Bond Energy = E for the process A2(g)  2A(g), i.e., a diatomic molecule
breaking homolytically into two atoms. These values are positive because it takes energy
to break the (covalent) chemical bond. In the table, Be2 and Ne2 have not been reported,
so there is no experimental determination of these values.

Also note that both Be2(g) and Ne2(g), which have bond orders of 0 (“no net bond”) have
been experimentally characterized, although their bond distances are long and, perhaps
more importantly, their bond energies are exceedingly small when compared to the other
diatomic molecules in the table.

The energies of MOs relative to the AOs that form them depend on the interatomic
distance: the energy difference between bonding and antibonding MOs decreases as the
distance increases. We can see this effect by the colors of the halogens: F2 is colorless;
Cl2 is yellow-green; Br2 is red-brown; and I2 is violet. The color arises because these
molecules absorb light of different frequencies that depends on the energy difference
between the highest occupied MO and the lowest unoccupied MO. The ground state
electronic configurations of the halogens are (s)2(*s)2(p)4(p)2(*p)4(*p)0, so the

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-47

electronic transition that occurs is from the -antibonding MO to the -antibonding

orbital, i.e., the excited state configuration becomes (s)2(*s)2(p)4(p)2(*p)3(*p)1.
Going from F to I, the distance between the atoms steadily increases. Therefore, the
energies of the antibonding orbitals relative to the p AOs on the halogen atom steadily
drop. This change affects the appearance of the halogens: fluorine absorbs light in the
UV region and appears colorless (letting all visible light through); chlorine absorbs high
energy visible light (ca. blue) and appears green-yellow; bromine absorbs lower energy
visible light (green) and is red-brown; iodine absorbs the lowest energy visible light (red)
and appears violet. This is a demonstration that molecules do show discrete energy
levels.
*2p

*3p
UV
*4p
551 nm
*5p
*2p 650 nm
*3p 730 nm
*4p
*5p
Energy of np AOs

5p
4p
3p 5p
2p
4p

3p

2p

F2 Cl2 Br2 I2
(Colorless) (Yellow-Green) (Red-Brown) (Violet)
144 pm 192 pm 228 pm 266 pm

Demonstration: “Singlet Oxygen” O2 is a paramagnetic molecule (it is attracted to the

poles of a magnet). This is a demonstration of unpaired electrons. O2 has 2 unpaired
electrons in its ground state, which is called “triplet” oxygen. We can obtain excited
states by creating O2 with all of its electrons paired – called “singlet” oxygen. We can
form singlet oxygen by reacting hydrogen peroxide in an aqueous solution with Cl2(g)
according to the reaction:

Cl2(g) + H2O2(aq) 
OH
 O2*(g) + 2 HCl(aq)

Hydrogen peroxide (H-O-O-H) already contains an O-O bond, so it is nicely set up to

create the oxygen molecule. In this reaction, Cl2(g) acts as a “base” and pulls protons
(H+) from hydrogen peroxide. This leaves O2(g) in an excited state. The other product is
hydrochloric acid, so we added hydroxide to the aqueous solution to encourage the
reaction to occur.

(NOTE: the name “triplet” oxygen comes from the spin states available to the molecule
from the electron spin. The ms quantum numbers for electron spin are +1/2 and 1/2,
which means that the electron spin s = 1/2 (this is like the orbital quantum numbers l and
m, where m = +l, +l1, …, l+1, l). For the (p*)2 configuration, we can have the
following microstates (combinations of electrons): (ms = +1/2, ms = +1/2), (ms = +1/2, ms
= 1/2), (ms = 1/2, ms = +1/2), (ms = 1/2, ms = 1/2). For each of these the sum of the

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-48

two spin quantum numbers (MS) is, respectively, +1, 0, 0, 1. The sum is called the
“total electron spin,” and we have S = 1, MS = +1, 0, 1 (triplet (three) state), and also S
= 0, MS = 0 (singlet (one) state).)

(e) Three-Center Bonding: Molecular orbitals extend over the entire molecule, so we can
think about chemical bonds that involve more than just two atoms. The next step is to
consider 3 atoms – there are 2 limiting structures: (i) triangle; (ii) linear. The molecular
orbital patterns for each are shown below:

Three-Center, Two- Three-Center, Four-

Electron Bond: H3+ Electron Bond: H3

1 Antibonding MO
2 Antibonding MOs (2 nodes);
(1 nodes);
1 Nonbonding MO
(1 node);

1 Bonding MO 1 Bonding MO
(0 nodes) (0 nodes)

Bond Order = 1/3 Bond Order = 1/2

A modification of the definition of bond order is as follows:

Bond Order = [(# electrons in bonding MOs  # electrons in antibonding MOs) / 2] / (# contacts)

For these cases of three-center bonding, # contacts = 3.

Three-center, two-electron bonding: when atoms do not have enough electrons to form
two-center, two-electron bonds (as found most molecules like H2 or N2, etc.), then the
best use of their valence electrons is by multi-center bonding. This is a common mode of
bonding in metallic solids, and may be considered as “metallic bonding.” The bond order
indicates that such three-center bonds are not a formally strong as two-center bonds:
Bond order = [(20)/2]/3 = 1/3.

Three-center, four-electron bonding: two electron pairs for two bonds seem conventional.
However, if the bonds share a common central atom, the structural arrangement is linear,
and the central atom has just single orbital available for chemical bonding in this
direction, then we find this special bonding scenario. The bonding orbital has
contributions from all three atoms, but the nonbonding orbital only has contributions
from the “terminal atoms,” i.e., those on the ends of the structure. Such bonding is
favorable when these terminal atoms are electronegative (i.e., F, O, Cl) and not favorable
when they are electropositive (i.e., Li, Be, even H). The bond order in this case is
[(20)/2]/2 = 1/2. This mode of bonding will become important when we examine
hypervalent molecules, i.e., molecules where is appears that the octet rule (see below) is
broken.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-49

(2) Molecular Geometry

(a) Lewis Structures allow chemists to write molecular structures in a way that identifies
areas of chemical reactivity and electronic behavior. They are useful for main-group
covalent molecules and solids, but are not viable for metallic systems. Such structures
can also give predictions of bond distances and bond angles.

To write a Lewis structure, we rely on the Lewis-dot structures of the main-group

elements:
H He

Li Be B C N O F Ne
We also use the octet rule, which simply states that main-group elements (whose valence
atomic orbitals are s and p orbitals) achieve stability when they are surrounded by 8
valence electrons, i.e., 4 valence electron pairs. H requires just a single electron pair (2
electrons) because it belongs to the first period. This “rule,” however, is inappropriate
for transition metals because these elements have d orbitals that can be involved in
chemical bonding.

Electron pairs in main-group molecules will be either bond pairs or lone pairs. Bond
pairs involve the overlap of two AOs on different atoms to form a bonding and an
antibonding MO. To be a stable bond, the bonding MO will be filled; the antibonding
orbital will be empty. Lone pairs are located at atomic sites, and are nonbonding MOs.
They can arise in one of two ways: (a) the AO is strictly nonbonding because there are no
AOs on adjacent atoms with which it can overlap; or (b) two lone pairs arise because both
the bonding and antibonding MOs are filled. In a Lewis structure, these different types of
electron pairs are symbolized as follows:

FF
For the homonuclear, main-group diatomic molecules, we have the following Lewis
structures:

Electronic configuration = (s)2. Each H atom has 1 valence electron; the H2

H H molecule has one bond pair and no lone pairs.

Electronic configuration = (s)2(*s)2(p)2(p)4(*p)4. One bond pair arises from

FF the p MO with 2 electrons; the corresponding *p is empty. Six lone pairs
arise from s and p bonding and antibonding MOs being filled.

Electronic configuration = (s)2(*s)2(p)2(p)4(*p)2. Two bond pairs arise from

the p MO with 2 electrons, the corresponding *p is empty; and the p MOs
O=O with net 2 bonding electrons Four lone pairs arise from s and one p bonding

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-50

and antibonding MOs being filled. The Lewis structure gives no indication of
unpaired spins.

Electronic configuration = (s)2(*s)2(p)2(p)4. Three bond pairs arise from the

NN p MO with 2 electrons, the corresponding *p is empty; and the p MOs with
net 4 bonding electrons Two lone pairs arise from s bonding and antibonding
MOs being filled.

Rules for Writing Lewis Structures:

1. Create the skeleton showing how the atoms will be connected to give the final
molecular structure. As a rule of thumb, the most electronegative elements are
found on the extremities of molecules, the more electropositive elements are
found on the interior. Thus, F, Cl, O are typically on the outer regions, B, C, N,
Si, P, etc. are in the interior. H (with just one valence AO) is also found on the
exterior.
2. Count the total number of valence electron pairs, taking into account the overall
net charge of the molecule. The number of valence electrons contributed by an
atom corresponds to its group number, e.g., B has 3 electrons, C has 4 electrons,
N has 5 electrons, O has 6 electrons, etc. The number of pairs is the total number
of valence electrons divided by two.
3. Draw a single covalent bond between each pair of atoms that are connected; this
utilizes one electron pair for each line drawn.
4. Complete an octet of electrons around the “terminal atoms” (those at the
extremities of the molecule) by placing lone pairs (nonbonding orbitals assigned
to a single atom); utilize multiple bonds if the inner atoms do not establish an
octet of electrons by shifting lone pairs or using the remaining pair of electrons; if
there are several possible Lewis structures, then see if resonance can be
established.
5. Calculate formal charges at each element:

Formal Charge = # valence e (neutral atom)  # valence e at atom in Lewis structure.

To count the # of valence electrons around the element in the Lewis structure, a
lone pair counts as two; a bond pair counts as one (the electrons in a bond pair
are equally shared by the two atoms). NOTE: the sum of all formal charges in the
Lewis structure equals the total charge on the molecule.

In addition, Linus Pauling (1954 Nobel Prize in Chemistry; 1962 Nobel Peace
Prize) included two additional corollaries (“rules”):

5a. Adjacent Charge Rule: Lewis structures that place electric charges of the same
sign on adjacent atoms make little contribution to the normal state of the
molecule.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-51

5b. Electroneutrality Rule: In general, the electronic structure of a substance is

such as to cause each atom to have essentially zero resultant charge, which has
been interpreted to mean that the best Lewis structures have the smallest formal
charges at each atom, i.e., close to or equal to 0.

Examples:

(1) NH3, ammonia: the skeleton has a central N atom surrounded by three H atom. The
total number of valence electrons is 5 + 3(1) = 8, or 4 pairs. Three pairs are used to
form three N-H covalent bonds and the fourth pair is a lone pair at N so that it
achieves an octet of electrons (three bond pairs + one lone pair):

H H H

N N N
H H H H H H
Skeleton of the molecule. H First, we connect the 3 NH by a Finally, we add a lone pair of
atoms need just 1 electron pair; N bond pair. This provides the electrons at the N atom. Now, N
atoms need 4 pairs, so N is at the bonding skeleton that holds the satisfies the octet rule, and we
interior. This picture represents atoms together to form the have accounted for all four
the symmetry of the molecule, molecule. These account 3 out electron pairs.
but gives no further details about of the 4 electron pairs. H atoms
how the ammonia molecule are satisfied; the N atom does not
appears. yet satisfy the octet rule.

The formal charge on N = 5  (2 + 31) = 0; the formal charge on H = 1  (1) = 0.

Using electronegativities (N = 3.0, H = 2.1), the N-H bond is polar covalent:
N3H+ -- so, the “formal charge” is not an assessment of electron distributions – it
is used for “bookkeeping” purposes. (NOTE: formal charges are different from
“oxidation states,” which reflect the hypothetical charge held by atoms in a molecule
or solid, assuming that electrons are completely held by these atoms. For example, in
ammonia the oxidation state of N is 3 and of H is 1+ because N (3.0) is more
electronegative than H (2.1).)

We can also use an orbital interpretation: for each bond pair in a Lewis structure,
there is a bonding/antibonding pair of orbitals (except for three-center, four-electron
cases, which arise later). The bonding orbital is filled; the antibonding orbital is
empty. Lone pair orbitals are filled with 2 electrons and have energies near the AO
energies from which these orbitals originate. Finally, keep in mind the relative
strengths of AO overlap:  > . Such orbitals in molecules are called localized
orbitals, because they are restricted to specific regions of a molecule. In the
following, we will abbreviate these orbitals as “MOs,” which stands for molecular
orbitals. However, molecular orbitals arise from solutions to the Schrödinger wave
equation; localized orbitals do not.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-52

So, for ammonia, we expect 3 N-H -bonding MOs, 1 N lone pair MO and 3 N-H *-
antibonding MOs. There are a total of 7 MOs (which agrees with starting from the
AOs: 4 on the N atom (2s and 2p) and 1 one each H atom), and 4 are occupied. The
nonbonding N lone pair MO is the highest occupied molecular orbital (HOMO); one
of the antibonding NH * MOs is the lowest unoccupied molecular orbital
(LUMO). The chemistry for ammonia involves this lone pair of electrons – it is
typical that chemical activity utilizes either the HOMO or the LUMO or even, both.

N-H *-antibonding MOs

N lone pair (nonbonding MO)


8e
N-H -bonding MOs

(2) Acetylene, C2H2: the skeleton is a linear chain of H C C H. The total number of
valence electrons is 2(4) + 2(1) = 10, or 5 pairs. Three pairs are used to form two C-
H bonds and one C-C bond, leaving 2 extra pairs. In order to achieve an octet at each
C atom, we need to place both additional pairs as bond pairs between the C atoms, to
form a carbon-carbon triple bond:

H C C H H C C H H C C H
The skeleton. H atoms at the First, we connect the 2 CH and Finally, we add 2 additional bond
exterior; C atoms interior. The 1 CC by a bond pair. This pairs between C atoms (“triple
molecule is linear, but there is no provides the bonding skeleton bond”). Now, C satisfies the
reason to accept that now. that holds the atoms together to octet rule, and we have
form the molecule. These accounted for all five electron
account 3 out of the 5 electron pairs.
pairs. H atoms are satisfied; the
C atom does not yet satisfy the
octet rule.

Formal charges at all zero; oxidation states are 1+ for H, 1 for C (C (2.5) is more
electronegative than H (2.1)). For a MO diagram, there are 10 AOs, so there must be
10 MOs. These MOs are: (i) 2 C-H -bonding MOs; (ii) 1 C-C -bonding MO; (iii)
2 C-C -bonding MOs; (iv) 2 C-C *-antibonding MOs; (v) 1 C-C *-antibonding
MO; and (vi) 2 C-H *-antibonding MOs. The HOMOs are the -bonding MOs; the
LUMOs are the *-antibonding MOs.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-53

2 C-H and 1 C-C *-antibonding MOs

2 C-C *-antibonding MOs

2 C-C -bonding MOs

2 C-H and 1 C-C -bonding MOs

(3) C2H2Cl2 (Dichloroethylene): the skeleton involves a central C C unit, with the two Cl
atoms and two H atoms connected at the ends. The number of valence electrons is
2(4) + 2(1) + 2(7) = 24, or 12 pairs. Five pairs are used to form covalent bonds: two
C-H bonds, two C-Cl bonds, and 1 C-C bond. Six pairs are needed to complete the
octet around each Cl atom, which leaves one electron pair to be accommodated
between the carbon atoms. This creates a carbon-carbon double bond:

Cl H
C C (trans isomer)
H Cl

Since H and Cl both use one electron to form covalent bonds with a neighboring
atom, there are two other possible isomers for this molecule:

H H H Cl
C C (cis isomer) C C (syn isomer)
Cl Cl H Cl

2 C-H * antibonding MOs

1 C-C * antibonding MO
2 C-Cl * antibonding MOs

1 C-C * antibonding MO

1 C-C  bonding MO

6 Cl lone pair MOs

2 C-H  bonding MOs

1 C-C  bonding MO
2 C-Cl  bonding MOs

The formal charges on all atoms is, again, 0, but the oxidation states are 0 for C, 1+
for H, 1 for Cl.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-54

(4) Resonance: The nitrate ion, NO3–: the skeleton involves a central nitrogen atom
surrounded by three oxygen atoms and an overall charge of 1. The number of
valence electrons is (5) + 3(6) + (1) = 24, or 12 electron pairs (we need to include the
negative charge to the contribution of valence electrons). Three pairs form three N-O
bonds. We can use the nine remaining pairs to complete the octets at each oxygen
atom, but then the nitrogen atom will not have an octet. Therefore, we must take one
lone pair from one oxygen atom and form a nitrogen-oxygen double bond. But, since
it does not matter with which oxygen atom we do this, we need to consider the three
possibilities:
–1 –1 –1
O O O

N N N
O O O O O O

These three Lewis structures are called resonance structures, and are needed to
completely describe the electronic structure of the nitrate ion. The formal charges
and oxidation states are as follows:

N: 5  4 = +1 +5
O (two lone pairs + 1 double bond): 6  6 = 0 2
O (three lone pairs + 1 single bond): 6  7 = 1 2

NOTE: adding up formal charges or adding up oxidation states gives the total charge
of the molecular ion as 1. Furthermore, the bond order of the NO is between a
single and double bond: we can calculate it as 4/3 = 1.33 (by adding up 4 bond pairs
distributed over 3 contacts).

The molecular orbital energy diagram can be constructed from a single Lewis
structure: there will be 3 NO  bonding and antibonding MOs; 1 NO  bonding
and antibonding MOs; and then 8 nonbonding, lone pair MOs at O atoms. Unlike the
NO  bonding MOs, this one  bonding MO involves all atoms in the nitrate
molecular ion. In other words, the electron density is delocalized over all atoms; such
delocalized orbitals are a signature of resonance structures. In NO3, the HOMO will
be among the O lone pair orbitals; the LUMO is the NO * antibonding MO. At the
nitrate ion, very little chemistry takes place near the N atom; it takes place near the O
atoms (as a weak base).

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-55

3 N-O * antibonding MOs

1 N-O  antibonding MOs

8 O lone pair MOs

1 N-O  bonding MO
(delocalized)

3 N-O  bonding MOs

The nitrate ion (NO3) is a planar ion. The resonance structures shown in the last
lecture are consistent with this structure. Is there anything wrong with the following
Lewis structure?
O

N
O O

This is certainly an acceptable Lewis structure from the point of view of keeping the
“octet rule” at every atom and taking into account 12 electron pairs. But, the lone
pair of electrons at the N atom forces the N atom to be out of the plane of the three O
atoms, and would suggest that the molecular ion is a pyramid.

(5) The isocyanate ion, OCN, is an important ion in polymer chemistry. What is its
Lewis structure? The number of valence electrons is (6 + 4 + 5 + 1) = 16 valence
electrons or 8 electron pairs. The following Lewis structures are possible, each of
which satisfies the octet rule at every atom:

O C N O C N O C N
+1 0 –2 0 0 –1 –1 0 0

We can calculate the formal charges for each Lewis structure:

(Left) O: 6  5 = +1 (3 bond pairs + 1 lone pair)

C: 4  4 = 0 (4 bond pairs)
N: 5  7 = 2 (1 bond pair + 3 lone pairs)

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-56

(Middle) O: 6  6 = 0 (2 bond pairs + 2 lone pairs)

C: 4  4 = 0 (4 bond pairs)
N: 5  6 = 1 (2 bond pairs + 2 lone pairs)

(Right) O: 6  7 = 1 (1 bond pair + 3 lone pairs)

C: 4  4 = 0 (4 bond pairs)
N: 5  5 = 0 (3 bond pairs + 1 lone pair)

Although all three Lewis structures satisfy the octet rule, the one on the left gives a
formal charge of +1 to oxygen. Since electronegativity increases from C to N to O,
the two on the right are better representations of the electronic structure, with the
right one being the best (1 formal charge on the most electronegative O atom).

(6) Benzene, C6H6, and its derivatives are important components of organic materials,
and often provide special properties. Two resonance structures are needed to describe
the electronic structure. Such examples of organic compounds are termed aromatic
compounds.
H
Benzene contains 6 carbon atoms in a six-
H C H membered ring. Each C atom is connected
C C
to 1H atom and 2 carbon atoms. There are
C C 30 valence electrons. 6 CH and 6 CC
H C H
bonds use 12 pairs. The remaining 3 pairs
H form double bonds, and there are two ways
to do this.

For benzene, often the carbon and hydrogen

atoms are not drawn, as shown here. The
CC bond order is 1.5 (9/6).

Limitations of Lewis Structures: Lewis structures are especially powerful descriptions of

molecules containing main group elements, but this simplified picture also has some
limitations. As one example, we have already seen that the Lewis structure of O2 (O=O)
gives no indication of any unpaired electrons. Here are some other examples…

(7) Carbon monoxide, CO, has 10 valence electrons = 5 valence electron pairs. CO is a
heteronuclear diatomic molecule, so the MO energy diagram shown earlier can be
used to establish a ground state electronic configuration. CO has the same number of
valence electrons as N2, so its configuration is (s)2(*s)2(p)2(p)4; the bond order is 3
(triple bond).

C O

Although the Lewis structure satisfies the octet rule at the C and O atoms, the formal
charges do not agree with electronegativities. Nevertheless, the formal charges do

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-57

agree with the experimental polarity based on dipole moment, which shows a small
value of 0.122 Debye. In fact, accurately calculating the dipole moment of CO has
been a great challenge to quantum mechanics – many of the first calculations
predicted a bond polarity opposite to experiment but consistent with
electronegativities.

(8) Hypervalent molecules involve atoms that are seemingly surrounded by more than an
octet of valence electrons as in, e.g., the P atom in PF5 or the S atom in SF6.

F F
F F F
P F S
F F F
F F

Note that the octet rule is satisfied at the F atoms, but P has 10 valence electrons and
S has 12 valence electrons surrounding them in these Lewis structures. Nevertheless,
the formal charges of all atoms in these Lewis structures are 0.

(9) The oxyanions, PO43, SO42, and ClO4, present particularly controversial Lewis
structures. If the octet rule is rigidly adhered to all atoms, then the only satisfactory
Lewis structure for each is

3 2 
O O O
+ 2+ 3+
O P O O S O O Cl O

O O O

The formal charges at the central atom, however, seem to violate electronegativity
concepts: Cl has the highest positive formal charge, while P has the lowest. Let’s
consider just the sulfate ion, SO42. If we consider the electroneutrality rule, then
other Lewis structures that must be considered include
2
O
0
O S O

O
which have 6 resonance forms. However, S now violates the octet rule.

A particularly interesting case is the recently discovered orthonitrate ion, NO43-,

which has been discovered in Na3NO4 and K3NO4 and characterized by X-ray

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-58

diffraction and infra-red spectroscopy (see Angewandte Chemie, Vol. 89, P. 567,
1977 and Zeitschrift fuer Anorganische und Allgemeine Chemie, Vol. 491, Pp. 175-
183, 1982). The only acceptable Lewis structure would be

3
O
+
O N O

O
which is in good agreement with the observed NO bond length of 1.398 Å (see part
(c) below).

(b) Hybridization: combination of atomic orbitals at a single site to create “localized”

orbitals (anisotropic) to represent distribution of electron pairs (bond pairs and lone pairs)
around a single atom, and, therefore, an explanation for observed geometries at atoms.
There are fundamentally three types of hybridization for the main-group elements: (1) sp;
(2) sp2; and (3) sp3. Such orbitals are also called bond orbitals.

NOTE: there is no evidence, either experimentally or theoretically for hybridization

involving d atomic orbitals among the main group elements! This fact is regularly
ignored in general chemistry textbooks.

The enhanced lobes are

+ directed in opposite directions,
creating a naturally linear
sp +
arrangement of electron pairs.

There remain two p orbitals
s px 
directed perpendicular to these
directions. The bond angle at
atoms involved in sp
hybridization is 180.

The enhanced lobes are

directed toward the points of an
equilateral triangle, creating
angles of 120. There remains
sp2 1 p orbital directed perpendi-
cular to the plane of these three
orbitals. The bond angle at
s px py
atoms involved in sp2
hybridization is ca. 120.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-59

The enhanced lobes are

directed toward the points of a
regular tetrahedron. All s and p
sp3 orbitals are used to form these
s px hybrids. The bond angle at
atoms involved in sp3
hybridization is ca. 109.5.
pz
py

Below two examples of hybridization are given. The first is for the molecule, ethene, H2C=CH2.
In this molecule, there is a double bond made between the two carbon atoms in the following
way. Three of the p orbitals of the carbon are hybridized with an s orbital to form 3 sp2 orbitals.
Two of these orbitals are used to form a sigma bond with a hydrogen atom. The other is used to
form a sigma bond with the other carbon atom (a). The unhybridized p orbitals on each carbon
form a pi bond (b). The total bonding configuration is illustrated in (c)

From this example, you should be able to generalize and describe the bonding in the molecule,
hexatriene: CH2=CH–CH=CH–CH=CH2. (It should be understood that the horizontal lines
represent bonds between the carbons in this notation.) The pi-bonding framework of this
molecule looks like:

In the figure above, only the unhybridized p orbitals on the carbons are shown, i.e., the ones that
are involved in forming the pi bonds in the double bonds. This is a very important bonding
configuration. When there are alternating double bonds, and the p orbitals forming them are all
perpendicular to the same plane, we say that the system is “conjugated” and that the electrons in

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-60

the unhybridized p orbitals are “free” to travel along the length of the conjugated system. In other
words, the molecule forms a “box” in the sense of the particle-in-the-box problem we discussed
earlier; and the length of this box determines where the molecule absorbs light. (There are six
unhybridized p orbitals in this example, thus there are six electrons that are delocalized along the
length of the “box.”)

Another example is given by acetylene, HC≡CH. In this molecule, each carbon atom forms two
sp orbitals by hybridizing one p orbital with one s orbital. One of these hybrid orbitals forms a
sigma bond with a hydrogen atom; the other, a sigma bond with the neighboring carbon atom (a).
The two remaining unhybridized p orbitals on each carbon are used to form two pi bonds (b).
The result is given in (c).

Can you work backwards and describe the bonding in CH4?

These drawings are taken from Chang’s text on general chemistry, Essential Chemistry. An
excellent introductory book on bonding is that by Companion, Chemical Bonding.

(c) Bond Distances vs. Bond Order: The distances between atoms depend on the sizes of
the atoms involved and on the strength of the forces holding the atoms together. With
Lewis structures, the concept of bond order corresponds, simply, to the number of bond
pairs between two atoms. Bond order often correlates with bond strength, which is
measured by the energy required to break the chemical bond. Also, bond order can
correlate with bond distance, but this is sometimes less exact because of the presence of
lone pairs, which can also affect the distances between atoms. The following table lists
various bonds among C, N, and O atoms, their bond orders and distances:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-61

Bond Type Bond Bond Distance Bond Type Bond Bond Distance
Order (pm) Order (pm)
N N
C C 1 1 147
154

C C 2 134 N N 2 124

C C 3 120 N N 3 110

N O 1 136
C N
1 143

C N 2 138 N O 2 122

C N 3 116 Nitrate 1.33 121

C O
1 143

O O
C O 2 123 1 149

3 113 O O 2 121
C O

Certainly, as the bond order increases, the bond distance decreases. But, notice that the
CN single bond is shorter than the NN single bond – this is due to the presence of a
lone pair on each N atom. These lone pairs add some extra electrostatic repulsion and
cause the distance to increase compared to what might be expected.

(d) Valence Shell Electron Pair Repulsion (VSEPR) model (Nyholm-Gillespie Model):
While Lewis structures give us an indication of how electrons can be distributed
throughout a molecule, we would like to use this information to understand the shapes
and geometrical structures of molecules, because these arrangements influence how
molecules behave – their physical and chemical properties. For main group (p-type)
elements, we can use the repulsion between electron pairs as a guide to predict molecular
structure. Essentially, around a (every) central atom in a molecular structure, we divide
space into electron pair domains. Atoms bonded to a central atom, i.e., terminal atoms,
are called ligands. The table below summarizes the rules and illustrates some examples.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-62

STRUCTURE EXAMPLE (LEWIS COMMENTS

STRUCTURE)
H FOUR bond pairs at the C atom. To
minimize the repulsion between the
Tetrahedral H C H electrons, they form a tetrahedron.
The four bond pairs are called four
electron pair domains.
H
FOUR electron pair domains
surround the N atom: three bond
pairs and one lone pair. Four
Pyramidal H electron pairs will arrange in a
tetrahedron, but there are only three
H N H bonds to atoms. The molecule is
not planar, but pyramidal.

THREE bond domains surround the

Trigonal Planar O C atom: two single bonds + one
double bond. The octet rule is
followed. This molecule is planar.
H C H
THREE bond domains at the N
N atom: one N-H single bond + one
Bent O H N-O double bond and one lone pair.
The lone pair forces the molecule to
be bent.

FOUR bond domains at the O atom:

types: two O-H single bonds and
O two lone pairs. These lone pairs
H H force the molecule to be bent.

TWO bond domains at the C

Linear O C O
atom: two C-O double bonds.
The molecule is linear.

The geometries for 5 and 6 pairs are illustrated below:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-63

AXIAL Ligands

90
EQUATORIAL
Ligands
120

Trigonal Bipyramid: 2 sets of ligands – Octahedron: all 6 ligands are equivalent; notice
equatorial ligands arrange in a trigonal planar that there are three linear arrangements of
manner; axial ligands are linear in a direction ligand-central atom-ligand. The angles are 90.
perpendicular to the equatorial plane. The
angles are shown.

To count electron pair domains around an atom, we must first draw its Lewis structure.
In this case, the octet rule is a useful guideline, but is not a rigid rule; in fact, it cannot be.
Use the following specific examples as guidelines for counting electron pair domains:

BeF2: 8 electron pairs – 6 lone pairs at F; 2 Be-F bond pairs. Be violates the
F Be F
octet rule, which is common for molecules containing Groups 1, 2 and 13
(Boron group) elements. Here, there are 2 electron pair domains
surrounding Be.

F BF3: 12 electron pairs – 9 lone pairs at F; 3 B-F bond pairs. B violates the
octet rule, which is common for molecules containing Groups 1, 2 and 13
B (Boron group) elements. Here, there are 3 electron pair domains
F F
surrounding B.

N
NH3: 4 electron pairs – 1 lone pair at N; 3 N-H bond pairs. N satisfies the
H
H octet rule, which is common for molecules containing Groups 14-16
H elements. Here, there are 4 electron pair domains surrounding N.

F PF5: 20 electron pairs – 15 lone pairs at F; 5 P-F “bond pairs”. P apparently

F violates the octet rule, but the linear F-P-F group utilizes 3-center bonding.
F P For the Lewis structure, nevertheless, we need 5 bond pairs. Here, there are 5
F electron pair domains surrounding P.
F
F SF6: 24 electron pairs – 18 lone pairs at F; 6 S-F “bond pairs”. S apparently
F F
violates the octet rule, but the linear F-S-F groups utilize 3-center bonding.
S
F F
For the Lewis structure, nevertheless, we need 6 bond pairs. Here, there are 6
F electron pair domains surrounding S.

# e Pair Domains: regions of electron pair density surrounding an atom. These can be
bond pairs (multiple bonds in a Lewis structure are treated as a single domain) or lone
pairs. We will limit our focus to 2-6 domains, but VSEPR considers even more cases.

Bond Pairs / Lone Pairs: #s of each surrounding an atom.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-64

Structure of Electron Pairs: how do the electron pair domains best arrange themselves
around an atom to minimize electrostatic repulsions between neighboring electron pairs?

Structure of Molecule: where are the bond pairs, or, where are the atoms? Our methods
do not allow us to directly observe lone pairs of electrons, but we can observe the
influence of lone pairs on molecular structure.

Hybridization: how do the atomic orbitals at the central atom combine to form
“localized” orbitals directed toward the places dictated by minimizing electron pair
repulsion?

The basic principle in VSEPR is that electron pairs will adopt an arrangement to minimize
electrostatic repulsions, which means that they maximize their mutual separations. For
2-4 electron pair domains, the hybridization schemes account for this response: linear for
2 pairs; trigonal planar for 3 pairs; and tetrahedral for 4 pairs. Molecular geometry is
further refined in the VSEPR model by assigning more space to lone pairs than to bond
pairs. Thus, the table below, the HNH bond angle in ammonia is 107, which is
smaller than the regular tetrahedral angle of 109.5. This decrease in bond angle is
attributed to the greater lone pair-bond pair repulsion than bond pair-bond pair repulsion.

# e Pair Bond Pairs / Structure of Structure of Example(s) Hybridization

Domains Lone Pairs Electron Molecule at Central
Pairs Atom

BeF2: 16 electrons
2 2/0 Linear Linear F Be F
(sp)(p)(p)

F-Be-F = 180; Nonpolar

CO2: 16 electrons (sp)(p)(p)

2 2/0 Linear Linear O C O

O-C-O = 180; Nonpolar

BF3: 24 electrons
3 3/0 Trigonal Trigonal F (sp2)(p)
Planar Planar
B
F F
F-B-F = 120; Nonpolar

O3: 18 electrons
3 2/1 Trigonal Bent O O (sp2)(p)
Planar O O O O
O-O-O = 117; Polar

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-65

CH4: 8 electrons
H
4 4/0 Tetrahedral Tetrahedral (sp3)
C
H
H
H
H-C-H = 109.5; Nonpolar

NH3: 8 electrons
N
4 3/1 Tetrahedral Trigonal H (sp3)
H
Pyramid H
H-N-H = 107; Polar

OH2: 8 electrons
4 2/2 Tetrahedral Bent O
(sp3)
H H
H-O-H = 104.5; Polar

PF5: 40 electrons
F
5 5/0 Trigonal Trigonal (sp2)(p)
F
Bipyramidal Bipyramidal F P
F
F
3 Equatorial F / 2 Axial F;
Nonpolar

SF4: 34 electrons
F
5 4/1 Trigonal “Sawhorse” F (sp2)(p)
Bipyramidal S
F
F
2 Equatorial F / 2 Axial F;
Polar

ClF3: 28 electrons
F
5 3/2 Trigonal T-shaped (sp2)(p)
F Cl
Bipyramidal
F
1 Equatorial F / 2 Axial F;
Polar

SF6: 48 electrons
6 6/0 Octahedral Octahedral F (s)(p)(p)(p)
F F
S
F F
F
Nonpolar

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-66

BrF5: 42 electrons
F
6 5/1 F F
Octahedral Square Br (sp)(p)(p)
Pyramid F F
4 Equatorial F / 1 Axial F;
Fax-Br-Feq = 84;
Br-Feq = 180 pm;
Br-Fax = 168 pm
Polar

XeF4: 36 electrons
6 4/2 Octahedral Square F F (sp)(p)(p)
Planar Xe
F F
F-Xe-F = 90; Nonpolar

Another issue to remember in the VSEPR model is how to arrange lone pairs for 5 and 6
electron-pair domains. Again, the primary issue is to minimize electrostatic repulsions,
and these repulsions decrease according to lone pair-lone pair > lone pair-bond pair >
bond pair-bond pair. For the 5 electron pair domain case with 4 bond pairs and 1 lone
pair, there is a choice for the location of the lone pair: equatorial or axial site.

OR

In the equatorial site, there are 2 lone pair-bond pair interactions at 90, but in the axial
site, there are 3 interactions. Therefore, the lone pair goes to the equatorial site, and the 4
bonds arrange themselves in the sawhorse structure.

F F F

F F
F P S F Cl
F F
F F F
Feq-P-Feq = 120 Feq-S-Feq = 101.6 Fax-Cl-Feq = 87.5
Fax-P-Feq = 90 Fax-S-Feq < 90 Fax-Cl-Fax = 175
Fax-P-Fax = 180 Fax-S-Fax = 173.1

P-Feq = 153.4 pm; S-Feq = 154.5 pm; Cl-Feq = 159.8 pm;

P-Fax = 157.7 pm S-Fax = 164.6 pm Cl-Fax = 169.8 pm

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-67

In these cases, the distances between the central atom and the axial ligand are greater than
the distances between the central atom and the equatorial ligand. The linear axial-central-
axial group is chemically bonded via a three-center, four-electron bond, which has a
bond order of 1/2; the equatorial-central group is bonded via a two-center, two-electron
bond, which has a bond order of 1. Furthermore, the lone pair(s) tends to occupy more
space, and push the bond pairs away from the strictly linear configuration (as seen in SF4
and ClF3).

To understand the chemical bonding in 5- and 6-electron pair domain cases: (a) linear
ligand-central-ligand groups involve 3-center, 4-electron bonds; (b) ligand-central groups
involve typical 2-center, 2-electron bonds. Therefore, for PF5, the three equatorial PF
bonds use sp2 hybrid orbitals at P to form 3 PF  bonds (3  bonding MOs + 3 *
antibonding orbitals). The two axial PF bonds use the remaining (unhybridized) p AO
at P to form 2 PF 3-center, 4-electron bonds.

Comments:

(1) Be and B often break the octet rule as seen in BeF2 and BF3. A Lewis structure that
fulfills the octet rule at Be or B by making Be=F or B=F bonds places a negative
formal charge at Be or B, which counters the concepts of electronegativity. Thus, in
these cases and their group relatives, we do not fulfill the octet rule, but keep them
hypovalent. Such molecules are reactive, and the Be or B atoms complete their octets
by getting electron pairs from neighboring molecules. Consider BH3, which contains
6 valence electrons (3 valence electron pairs). Its Lewis structure must violate the
octet rule at the B atom – only 3 electron pairs.
H

B
H H

B 3 BH bonds utilize 3 sp2 hybrid orbitals at B to

form 3 BH  bonding MOs (filled) and 3 BH *
H H antibonding MOs (empty).
H H
B B atoms can complete its octet by association of
H two BH3 molecules: an electron pair in a BH bond
B
H can be delocalized through overlap with the empty
p AO on the other BH3 molecule.
H H

H
H H
B B On association, we create B2H6; each B atom is
H H surrounded by a tetrahedron of 4 H atoms, and the
H octet rule is obeyed.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-68

(2) Using 3-center, 4-electron bonds at central main group elements in the trigonal
bipyramidal and octahedral arrangements does not violate the octet rule at the central
atom. Here is qualitative molecular orbital diagram for PF5:

3 P-F * antibonding MOs (from P sp2 hybrids)

1 F-P-F 3-center antibonding MO (from P p AO)

1 F-P-F 3-center nonbonding MO

15 F lone pair MOs

1 F-P-F 3-center bonding MO (from P p AO)

3 P-F  bonding MOs (from P sp2 hybrids)

In this picture, there are 4 bonding orbitals associated with the central P atom, which
agrees with the octet rule. PF5 has a total of 40 valence electrons (5 + 57), so we
must fill 20 MOs. These MOs involve 3 P-F bonding MOs in the equatorial plane, 1
F-P-F bonding MO along the axial direction, using just the P 3p AO, 15 lone pairs at
the 5 F atoms, and 1 F-P-F nonbonding MO along the axial direction, which involves
just AOs from the F atoms.

(3) Multiple bonds and lone pairs utilize more space than a single bond pair, and so can
affect bond angles. For the effect of lone pairs, we see the nearly tetrahedral angles
in NH3 and OH2 decrease steadily from ca. 107 to 104.5. For the effect of multiple
bonds, consider the molecule COCl2, the O-C-Cl bond angle is 124.3 while the Cl-
C-Cl bond angle is 111.4.
O
124.3
C
Cl Cl
111.4

(4) Bond distance issues: (a) O-O distance increases from O2 to O3 to H2O2 (1.21, 1.28,
1.48 Å). This is just another example of repulsion between lone pairs on adjacent
atoms; (b) Distances in 3-center, 4-electron bonds are typically longer than in typical
single bonds (2-center, 2-electron bonds). Recall that the bond order in 3-center, 4-
electron bonds bonds is 1/2; the bond order in a 2-center, 2-electron bond is 1.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-69

(5) The Ligand Close Packing (LCP) concept. In recent years, the VSEPR model has
been refined to provide quantitative predictions of molecular geometry, especially
bond angles. The LCP concept states that atoms (ligands) bonded to a central atom
have a fixed radius, and the bond angles adjust until these ligands (modeled as
spheres) are just touching, i.e., “close packed.” Thus, bond lengths are determined by
atomic / covalent radii; bond angles are determined by lone pair electrons repelling
bond pairs until the ligands just touch. Consider the triatomic molecules OH2, OF2,
OCl2:
OH2 OF2 OCl2
140.5 pm 169.6 pm
95.8 pm
103.1 110.9
104.5

151.4 pm 220.1 pm 279.3 pm

R(H) = 76 pm R(F) = 110 pm R(Cl) = 140 pm

The HOH and FOF bond angles are both smaller than 109.5, which is expected
if the lone pairs occupy more space than the bond pairs surrounding the O atoms.
However, in OCl2, the ClOCl is larger than 109.5. Notice that the bond distances
increase along the series. The radii for H, F, and Cl listed are specifically the
nonbonded radii for each atom. Furthermore, the nonbonded radius of the O atom is
not available from these examples: O is involved in polar covalent bonding and the
electron densities for H, F, or Cl overlap those of O, as also depicted.
The value of this method is in predicting bond angles. For example, what would you
expect the HOF bond angle to be in HOF? the HOCl bond angle to be in HOCl?

HOF HOCl
144 (141) pm 169 (170) pm
96 (96) pm 98 (96) pm

213 (216) pm
183 (186) pm

HOF = 97.3 (101.7) HOCl = 102.6 (105.2)

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-70

Experimentally determined distances and angles are shown; the predictions from LCP
are in parentheses. LCP slightly overestimates these bond angles, but the assumption
that the bond distances are transferrable between molecules is not entirely valid.
Nonetheless, the agreement with experiment is quite good, and the relationship
between the two examples is correct.

What do you expect for the bond angle in FOCl? Answer: 106.6. This molecule
has not been structurally characterized (OClF is more stable), but quantum
chemical calculations give FO = 146.2 pm, OCl = 170.4 pm, and FOCl =106.0.

(3) Bonding in Solids

Solids involve 1023 atoms, so we can think of solids as “quasi-infinite” molecules. In an

orbital picture, there are so many orbitals that they coalesce into quasi-continuous bands.
Metals are characterized by no forbidden energies for their wavefunctions;
semiconductors and insulators (nonmetals) have forbidden energies. The different types
of solids can be classified into one of three major categories based on their electrical
properties:

(a) Ionic Solids: In ionic solids (salts), the cations transfer their valence electrons to the
anions, and both achieve a stable, noble gas electronic configuration (octet of electrons;
four electron pairs in (ns)2(np)6). The interactions between ions are simply the
electrostatic attraction between positive and negative ions: this has no preferred
direction, so ionic solids tend to be close-packed solids. Salts are insulators (do not
conduct electricity), and have large energy gaps (greater than ca. 3 eV; MAX = 400 nm)
between their bonding and antibonding orbitals. The bonding orbitals are mostly on the
anion; the antibonding orbitals are mostly on the cation. The energy gap arises from the
electronegativity difference between the cation and anion. Most ionic solids are
transparent because all visible light is not absorbed. (NOTE: upon melting, ionic solids
will become conductive, but the mechanism is due to ion conduction (mobility) and not
electronic conduction.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-71

NaCl(s) The “anion orbitals” (also called the

valence band) are filled, so we
denote chlorine as “Cl”. The
“cation orbitals” (also called the
Energy Cation Orbitals
(Empty)
conduction band) are empty, so we
denote sodium as “Na+”. The “band
Cation AO gap” is the separation between the
filled (bonding) anion orbitals and
the empty (antibonding) cation
orbitals. 3 eV corresponds to
Electron
Transfer Band Gap NaCl(s) is a transparent wavelengths less than ca. 400 nm
(> 3 eV)
solid. (UV part of the spectrum.

Cl

Anion AO
Cl Na+ Cl
Anion Orbitals
(Filled)

Cl

(b) Covalent Solids: Electrons are tied up in covalent bonds. For example, silicon is a
3D network of Si bonded to four other Si atoms in a tetrahedral arrangement. Each bond
contains two-electrons. There are bonding and antibonding orbitals. In a semiconductor,
when light shines on the material, it can conduct, if the light has sufficient energy
(frequency). The basis behind the conducting properties of semiconductors is tied to the
distribution of orbitals in the solid. The Lewis-dot structure of Si involves four unpaired
electrons, so Si will form four covalent bonds with its neighbors. When these neighbors
are also Si atoms, the process will continue ad infinitum, i.e., for a very large number of
atoms. In the unit cell of Si (cubic: a = 5.43  10–10 m), there are eight Si-Si bonds, each
of which has a filled bonding molecular orbital and an empty antibonding molecular
orbital (see left side of figure below). In a solid sample of Si, which can be a cube of side
1.0 mm, there will be approximately 1020 Si-Si bonds in the material. For each bond,
there will be a molecular orbital, so we obtain the picture on the right (below).

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-72

Silicon The valence band originates

from Si-Si bonding
Energy molecular orbitals (filled);
the conduction band comes
from Si-Si antibonding
Conduction Band
Antibonding M.O. (Antibonding) molecular orbitals (empty).
The energy gap is controlled
by these interactions.
Si is a black solid.
Energy Gap

The structure of Si is
Valence Band
Bonding M.O. (Bonding) that of diamond.
Every Si atom is
surrounded by a
tetrahedron of four Si
Si-Si Si
Dimer Solid atoms.

The occupied set of orbitals (called the valence band) is completely filled; the
unoccupied set of orbitals (called the conduction band) is separated by an energy gap.
The size of the energy gap controls the amount of energy that will get this material to
conduct, because that energy will cause electrons at the “top” of the valence band to be
excited into the conduction band. This creates a mechanism for these electrons to move
throughout the material and create a current. This is accomplished by supplying a
voltage, or by electromagnetic radiation. Other examples in which the bonding is “polar
covalent” include GaN, GaAs, InP, ZnS, ZnSe.

(c) Metallic Solids: Elements like Na, Mg, Al are metallic and form close-packed
structures (lots of triangles, i.e., 3-center, 2-electron bonds). There is no energy gap
between the orbital that contains the last electron available and the first empty orbital.
Therefore, there already exists a mechanism for electrons to move throughout the solid –
temperature provides some kinetic energy to the electrons, and electrons near the highest
occupied orbitals (called the Fermi level in a metal) can be excited into the lowest
unoccupied orbitals. In these cases, the valence s and p AOs overlap and form one quasi-
continuous collection of orbitals.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-73

Sodium Sodium is a metal because there are

Energy empty electronic states just above the
filled states. These empty states provide a
mechanism for electronic conduction.
Conduction Here, there is no bandgap; the shiny
Band
appearance is a reflectance property of
p Na metal in oil. metals.

Fermi Level
s
Sodium adopts the bcc structure. The unit
cell is shown here.

Summary: The types of chemical bonding and solids are summarized below:

“Ionic” “Polar Covalent” “Covalent”

Types of Atoms High Electronegativity (F, Cl, Different Same Elements: CC;
forming the Bond O) with Low Electronegativity Electronegativities, but SiSi ; LiLi
(Li, Na, Ca) smaller difference: SiO,
HF, CH
E (Antibonding) Large: due to energy Medium-Large: energy Small-Large: energy
E (Bonding) difference between atomic difference between atomic from sharing electrons
orbitals orbitals PLUS energy
from sharing electrons
Energy Band ca. 500 kJ/mol (250 nm) ca. 100-400 kJ/mol ca. 20-100 kJ/mol
Gap in Solid
Properties Insulating; Conducting when Insulating to Semiconducting-
melted; Transparent Semiconducting; Metallic; Opaque,
Transparent-Colored Black

The different types of compounds and bonding types can be summarized in a van Arkel-
Ketelaar triangle, which uses electronegativity as a quantitative assignment to each
element:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-74

CsF
 (Pauling) = BA

Ionic

Polar
Covalent

Metallic Extended Molecular

Covalent Covalent
0
Cs  (Pauling) = BA)/2 F
(0.7) (4.0)

This diagram is simply a map. The horizontal coordinate is the average electronegativity
value of the elements in the substance; the vertical coordinate is the electronegative
difference between the elements in the substance. Pure elements sit along the base of the
triangle, starting with Cs on the left (lowest electronegativity among naturally occurring
elements) and ending with F on the right (highest electronegativity among these
elements). The most ionic compound, CsF, sits at the apex of the triangle because it has
the largest electronegativity difference while the average electronegativity is in the
middle (0.7 + 4.0)/2 = 2.3. An element like Si ( = 1.90) would be a point with
coordinates (1.90, 0). A compound, e.g., NaCl, is a point on this map with coordinates
(2.05, 2.23), since (Na) = 0.93 and (Cl) = 3.16. Current research interest lies in the
middle of the triangle because such compounds show potentially interesting properties
for applications, e.g., magnetic refrigeration, thermoelectricity, hydrogen storage (for fuel
cells), magnetoresistance, superconductivity, among other characteristics.

Polymers
READING: BLB-11, Ch. 12.6,7; 25 Probs:
BLB-12, Ch. 12.8; 24
PROBLEMS: --

(1) Functional Groups in Organic Molecules

Molecules consisting primarily of C, H, O, and N belong the discipline of organic

chemistry. Such compounds contribute to numerous natural processes, and understanding
the structural and chemical characteristics of such substances are important for many
different applications, e.g., medicine (pharmaceuticals) and materials (polymers), to name
just two. Here, we will summarize certain classes of organic compounds, based on the
important functional group in the molecule. A functional group is a collection of atoms

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-75

bonded together that is largely responsible for the chemical and/or physical behavior of
the molecule. For this class, it will be important to recognize the functional group and
corresponding compound class.

(a) Hydrocarbons: such compounds typically form the backbone for all organic
compounds. They consist of chains of carbon atoms (these chains can be “straight-chain”
or “branched”) with hydrogen atoms bonded to carbon to complete an octet of electrons
around every carbon atom.

(i) Alkanes: These compounds contain just single covalent bonds. Alkanes are also
called saturated hydrocarbons because they contain the maximum number of H atoms
that can bond with the number of C atoms present in the molecule. The environment
surrounding the C atom in alkanes is tetrahedral. Alkanes form the primary structural
backbone for every organic molecule – the number of carbon atoms dictates the
name:
H

1 C atom Methane CH4 H C H

H
C
H

H H H

H H H H
H
2 C atoms Ethane C2H6 H C C H C C
H
H H
H H

H H H H H

3 C atoms Propane C3H8 H C H

H C C C H
C C

H H H H H H H

H H H H H H H H

4 C atoms Butane C4H10 H C C

H C C C C H
C C H

H H H H H H H H

H CH3 H H H

“Isobutane” H C
H C C C H H
H C
H H H C CH

H H H H

    

In alkanes, every C atom is surrounded by a tetrahedron of atoms. With 4 C

molecules, we can begin to see different isomers, which are different structures with
identical chemical compositions. These different structures can significantly affect
physical properties of the substances.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-76

Alkyl groups are “functional groups” that provide the carbon framework for many
organic molecules and polymers. Removing one H atom from an alkane produces an
alkyl group; this group has one unpaired electron and is prepared to form a single
bond with other atoms, e.g., O, N, etc.
H

Methyl CH3 H C

H H

Ethyl C2H5 H C C

H H

H H H

H C C C

H H H

Propyl C3H7
-or-

H H H

H C C C H

H H

H H H H

H C C C C

H H H H

Butyl C4H9 -or-

H H H H

H C C C C H

H H H

(ii) Alkenes: These compounds contain C=C double bonds, and are an example of an
unsaturated hydrocarbon. The carbon atoms are trigonal planar coordinated; the
bond angles are close to 120. There is the possibility of different isomers: cis- and
trans-, which can impact properties of these molecules. Also, the C=C double bond
is the site of the chemistry for these compounds. In the example on the left, the Cl
atoms are arranged in a trans-arrangement with respect to the C=C double bond.
Such double bonds can also occur multiple times; in most naturally occurring

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-77

hydrocarbons and organic molecules, C=C double bonds will alternate with CC
single bonds.
Cl H H H

C C H
C C
H C C
H Cl
H H

(iii) Alkynes: These compounds contain CC triple bonds, and are another example
of an unsaturated hydrocarbon. The carbon atoms involved in triple bonds are
linearly coordinated; the bond angles are 180. Again, the CC triple bond is the site
of the chemistry for these compounds.
H

H C C C H

(iv) Aromatic: These compounds contain the phenyl group, C6H5, which is the
benzene ring with one H atom missing. The C atom at the site where the H atom is
missing has one unpaired electron and can form bonds with other functional groups,
including alkyl groups, etc. These phenyl groups often provide additional strength to
these chemical structures. The resonance structure in the benzene ring is often
symbolized by the hexagon with a circle inside, which represents electron
delocalization within the ring.
H

H
H C H
H C H
C C H C H
 C C
C C
H C H C C
H C H
H
H

Benzene (C6H6)
Toluene (C7H8 = C6H5CH3)

(b) Alcohols: These compounds contain the group OH, called a hydroxyl group, as in
methanol (CH3OH) or ethanol (C2H5OH). The presence of these hydroxyl groups allow
for hydrogen bonding to play important roles – these compounds can have higher boiling
and melting points than expected based entirely on dispersion forces. Alcohols are
important reactants to prepare other organic molecules.
OH
H
H C H
H C O C C

H
H C C
H C H

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-78

Methanol (CH3OH) Phenol (C6H5OH)

(c) Aldehydes and Ketones: These compounds contain a C=O double bond, also called a
carbonyl group; such compounds are often used as solvents, e.g., acetone, C3H6O, which
is (CH3)2C=O.

H O H O H

H C C H H C C C H

H H H

(d) Carboxylic Acids and Esters: These compounds contain a COO group, which
involves a C=O double bond and a CO single bond, also called a carboxyl group; in
acids, there is COOH, in esters, the H atoms is replaced by an alkyl group.

H O H O H

H C C O H H C C O C H

H H H

In carboxylic acids, the H atom bonded to the O atom can be removed as a proton (H+),
which leaves behind a negatively charged carboylate anion that is stabilized by two
resonance structures:
H O H O

H C C O H C C O

H H

The acetate ion, C2H3O2 = CH3COO, shows resonance stabilization via the carbon-
oxygen bonds.

(e) Amines: These compounds may be written as NRH2, NR2H, or NR3, and contain a N
atom that is bonded to one-, two-, or three hydrocarbon (R) groups. In the following
examples, the hydrocarbon group is a methyl group:

H H H H
H

H C N H H C N C H H C N C H

H H H H H H CH3 H

As for alcohols, the presence of N atoms with a lone pair allow for hydrogen bonding to
play a role in their chemical and physical properties. However, the effect is opposite
because the hydrocarbon groups bonded to the N atom will interfere with hydrogen
bonding effects due to their sizes.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-79

(f) Amides: These functional groups are the important linkages found in peptides and
proteins; they consist of a C=O double bond connected via the C atom with an amine N
atom, i.e., NHR.
H O H

H C C N C H

H H H

(2) Polymers: Structural Features

Polymers are molecular compounds with a large molar mass, which are 104-106 amus
(gram/mole = Dalton). A typical unit of molar mass for polymers is the kilodalton (1
kDa = 1000 amu). These compounds are also constructed of many repeating units, called
monomers. Monomers are the fundamental, small building units of the polymer, which
are covalently bonded together. When a few monomers are connected together,
oligomers are formed. As the process continues, we produce polymers.

In general, polymers are solids at room temperature and pressure. The main forces
holding polymer chains together are: (1) van der Waals (dispersion) forces, which are
numerous weak attractions that add up to provide considerable forces holding the
polymers together; (2) Hydrogen bonding, which can also be numerous; and (3) Covalent
bonds, which provide especially strong linkages between polymer molecules, known as
crosslinking, such polymers can be very strong materials.

Demonstration: An emulsion of latex in water resembles milk. The latex is composed

of ca. 35% (by mass) of natural rubber particles) and ca. 65% of water. Then, 6M
HCl(aq) is added. The result—latex rubber collects as a “spongy” polymer on the stirring
rod. It can be formed into a bouncing rubber mass. In this case, small molecular mass
molecules are hydrocarbons that are hydrophobic. The particles remain segregated until
the acid is added. Once the acid is added, coagulation occurs, and the product can be
squeezed and shaped into a ball. The acid provides the monomers and oligomers to
polymerize into chains; the resulting large molecular weight chains stick together via
dispersion forces to create the solid.

The monomers in natural rubber are called isoprene, which have the Lewis structure:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-80

CH3 H CH3
H H H C C H
=
C C C C H C C

H H H H

Upon polymerization (addition), the electron pairs in the carbon-carbon double bonds
rearrange to form a new carbon-carbon single bond, and a new carbon-carbon double
bond:

CH3
CH3
H H H Acid H H H
n C C C C
C C C C
H H
H H n

The polymer chains can be terminated by components of the acid, i.e., H or Cl atoms.
Since n can be several thousand, it does not take a lot of acid to accelerate this
polymerization reaction.

Crosslinking via covalent bonding occurs for rubber by tying together these new carbon-
carbon double bonds from different polymer chains. An effective reagent for polymer
crosslinking that was discovered by Goodyear was sulfur, which has a Lewis-dot
structure that has two unpaired electrons,
S
Then, two chains can be linked together by two sulfur atoms as follows:

CH3
H H H

C C C C

H H These S atoms use their unpaired electrons

S S to link two chains together. The C=C bond
H H is converted into a C–C bond.
C C C C

H H H
CH3
n

Demonstration: Crosslinking via hydrogen bonding takes place when sodium borate,
NaB(OH)4, is added to polyvinyl alcohol, (C2H3OH)n. At room temperature and
pressure, polyvinyl alcohol is a liquid, and is more viscous than water. When a small
amount of borax is added, the H atoms of the alcohol, i.e., the H atoms at the hydroxyl

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-81

groups, become hydrogen bonded to the oxygen atoms of the borate ions, and we get
“slime.”
H H H H

C C C C

H OH H OH
n
Vinyl Alcohol Polyvinyl alcohol

H H

C C

H O
n
H

OH
Crosslinking via hydrogen bonding
HO B O H
between the lone pairs on an O atom
with hydroxyl protons on the
polymer chains.
OH

H O

C C

H H
n

The microscopic structure of polymers can also affect properties. Polypropylene, C3H6,
has the Lewis structure from its monomer:

n C C C C

n
In the polymer, there are only single bonds. Each carbon atom is surrounded by four
carbon atoms in the shape of a tetrahedron, so the “CH3” (Me) group can have various
positions. The CC chain is, in fact, a zig-zag chain. There are three types of
polypropylene:
H H H H H H H H H H ISOTACTIC: All Me groups are on
the same side of the carbon chain.
Density is 0.95 g/cm3.
(Crystalline, dense solid: HDPP =
Me H Me H Me H Me H Me H high density polypropylene)

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-82

H H H H H H H H H H SYNDIOTACTIC: Me groups
alternate sides of the carbon chain.
Density is 0.95 g/cm3.
Me H H Me Me H H Me Me H

H H H H H H H H H H ATACTIC: No special arrangement

(random) of the Me groups with
respect to the carbon chain. Density
is 0.85 g/cm3.
Me H Me H H Me Me H H Me (Soft, less dense solid: LDPP = low
density polypropylene)

The two ordered (crystalline) forms of polypropylene show a higher density than the
disordered (amorphous) form. This arises because the attractive dispersion forces that
can readily bring the ordered polymer chains closer together (there is a smaller free
volume), than in the disordered chains. The denser polymers create harder materials.

(a) Major Applications of Polymers based on their structures include (Introductory reference:
Macrogalleria; http://pslc.ws/macrog/maindir.htm)

(i) Fibers: cellulose and nylon. Cellulose is a polysaccharide and forms by a

condensation of glucose in which water is a by-product. Nylon is a polyamide, and
also forms by condensation. Fibers are always made of polymers which are arranged
into crystals; the polymer molecules can pack into a regular arrangement, e.g., as in
nylon-6,6:

The hydrogen bonds and other secondary interactions between the individual chains
hold the chains together very tightly; i.e., so tightly that they do not “slide past one
another.” Therefore, when you pull on the nylon fiber, it does not stretch, and can be
used for rope or thread. This is why fibers are good for using as rope and thread.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-83

The mechanical properties of fibers can be represented on a stress-strain graph: stress

is a measure of the total internal forces in a structure per unit area (units of pressure);
strain is a measure of deformation, i.e., relative stretching, compressing, etc. (no
units). Compression is a form of stress (so the units of pressure = Newton/m2);
tension would be the opposite of compression, but has the same units. We also
distinguish strength from toughness:

Strength is the measure of force required to break a sample;

Toughness is the measure of energy required to break a sample.

On the stress-strain graph illustrated below, the strength of a ductile material is

related to the slope of the curve, while the toughness is related to the area under the
curve.

Source: IN-VSEE.htm
(Specific Link: http://invsee.asu.edu/srinivas/stress-strain/phase.html?x=154&y=13)

As a simple example, we can identify the strength and toughness of a polymer

according to the following scheme:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-84

Stress
High Strength

Moderate Strength; High Toughness

Low Strength; Low Toughness

Strain

In general, useful polymer fibers have good tensile strength (i.e., strong when pulled
or stretched), and they usually have poor compressional strength (i.e., weak when
compressed). Also, fibers tend to be strong only in one direction; the direction in
which they're oriented. If you pull in them in the direction at right angles to their
orientation, they tend to be weak.

Because of this combination of strengths and weaknesses, it is often useful to use

fibers with another material, such as a thermoset (another term for crosslinker). The
fiber compensates for the thermoset's weaknesses, but the thermoset's strengths make
up for the fiber's weaknesses as well. When a thermoset or any other polymer is
reinforced with a fiber like this, such materials are called a composite.

(ii) Foams: these melt congruently and can be molded and shaped. Polyurethanes are
the most well known polymers used to make foams, as found, for example, in chair
padding. In addition to producing foams, polyurethanes can be elastomers, paints,
fibers, and adhesives. An example of a polyurethane is spandex:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-85

One unusual polyurethane thermoplastic elastomer is spandex, which DuPont sells

under the trade name Lycra. It has both urea and urethane linkages in its backbone.
What gives spandex its special properties is the fact that it has hard and soft blocks in
its repeat structure. The short polymeric chain of a polyglycol, usually about forty or
so repeats units long, is soft and rubbery. The rest of the repeat unit, you know, the
stretch with the urethane linkages, the urea linkages, and the aromatic groups, is
extremely rigid. This section is stiff enough that the rigid sections from different
chains clump together and align to form fibers. Of course, they are unusual fibers, as
the fibrous domains formed by the stiff blocks are linked together by the rubbery soft
sections. The result is a fiber that acts like an elastomer. This allows us to make
fabric that stretches for exercise clothing and the like.

Polyurethanes have a urethane linkage in their backbones.

(iii) Elastomers: rubber. Show two different solid phases: a crystalline form
(hard/brittle) and an amorphous form (soft). The transition between crystalline and
amorphous solid phases occurs at the glass transition temperature:

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-86

T T
Crystalline Solid (Hard) 
g
 Glass (Soft) 
f
 Liquid

Tg is the glass transition temperature; Tf is the melting point of the solid.

Different polymers are used under different conditions. For example, hard plastics
like polystyrene and poly(methyl methacrylate) are used below their Tg values (both
ca. 100C).

CH2 CH

n
Polystyrene

Poly(methyl methacrylate) (PMMA), is a clear plastic used as a shatterproof

replacement for glass. The chemical company Rohm and Haas makes windows out of
it and calls it Plexiglas®. Ineos Acrylics also makes it and calls it Lucite. Lucite is
used to make the surfaces of hot tubs, sinks, one-piece bathtub/shower units, among
other things. The clear barrier at the ice rink which keeps hockey pucks from flying in
the faces of hockey fans is made of PMMA. PMMA has another advantage over
glass for making windows: PMMA has a lower index of refraction than glass.
Therefore, when glass windows are made too thick, they become difficult to see
through. But PMMA windows can be made as much as 13 inches (33 cm) thick, and
they're still perfectly transparent. This makes PMMA a wonderful material for
making large aquariums, with windows which must be thick in order to contain the
high pressure of millions of gallons of water. In fact, the largest single window in the
world, an observation window at California's Monterrey Bay Aquarium, is made of
one big piece of PMMA which is 54 feet long, 18 feet high, and 13 inches thick (16.6
m long, 5.5 m high, and 33 cm thick).

PMMA is also found in paint. The painting on your right, Acrylic Elf, was painted by
Pete Halverson with acrylic paints. Acrylic "latex" paints often contain PMMA
suspended in water. PMMA is often used as an additive to lubricating oils and
hydraulic fluids, which can become quite viscous when they get really cold. When
some PMMA is dissolved in these fluids, the composite lowers the viscosity, and
machines can be operated down to 100 oC.

Polyisobutylene (butyl rubber, PIB) is a synthetic rubber (a vinyl polymer) that is gas
impermeable, i.e., it can hold air for long periods of time. Balloons will go flat after a
few days, because they are made of polyisoprene, which is not gas impermeable.
Because polyisobutylene will hold air, it is used to make things like the inner liner of
tires, and the inner liners of basketballs.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-87

H CH3 H H H

C C C C C C

H CH3 H CH3 H
n n
Polyisobutylene Polyisoprene

If Tg of a useful polymer is too high for practical applications, we can add a

plasticizer, which is a small molecule which will get in between the polymer chains,
and space them out from each other. We call this increasing the free volume. When
this happens they can slide past each other more easily. When they slide past each
other more easily, they can move around at lower temperatures than they would
without the plasticizer. In this way, the Tg of a polymer can be lowered, to make a
polymer more pliable, and easier to work with. Examples of plasticizers include

NO2 S C S

Nitrobenzene Carbon disulfide

The so-called “new car smell” originates from a plasticizer evaporating from the
plastic parts on the inside of your car. After many years, if enough of it evaporates,
your dashboard, for example, will no longer be plasticized. Therefore, the Tg of the
polymers in your dashboard will rise above room temperature, and the dashboard will
become brittle and crack.

(iv) Conducting Polymers are organic polymers that can conduct electrical current.
Therefore, there must be a pathway for electronic delocalization. The earliest
example of a conducting, organic polymer was polyacetylene:

H H

C C
C C

H H
n n

As it turns out, due to this resonance structure and an alternation of C=C double
bonds and CC single bonds along the polymer chain, polyacetylene is a
semiconductor. But, when it is doped with a small amount of Br2, the Br atoms will
take a few electrons away from the chain, and it becomes electrically conducting.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-88

Energy

Conduction Conduction
Band Band

Energy Gap

Fermi Level

Valence Valence
Band Band

Polyacetylene Polyacetylene-Br

Conducting polymers have many uses. The most documented are include: (i)
corrosion inhibitors; (ii) compact capacitors; (iii) anti-static coatings; (iv)
electromagnetic shielding for computers; and (v) “smart windows” (for energy
efficiency). A second generation of conducting polymers are also uses for (i)
transistors; (ii) light emitting diodes (LEDs); (iii) lasers used in flat televisions; and
(iv) solar cells.

(v) Another example includes Teflon, which represents a series of perfluorinated

alkenes originally discovered while searching for new refrigerants.
Polytetrafluoroethylene (PTFE) is a white solid at room temperature, with a density
of ca. 2.2 g/cm³. Its melting point is 327 °C, but its properties degrade above 260 °C.
PTFE's coefficient of friction is no larger than 0.1, which is the lowest of any known
solid material, and finds its use as non-stick coating. It also cannot be cross-linked.

PTFE has excellent dielectric properties, especially at high radio frequencies, making
it suitable for use as an insulator in cables, connector assemblies, and for printed
circuit boards used at microwave frequencies. Combined with its high melting
temperature, this makes it the material of choice as a high-performance substitute for
the weaker and lower melting point polyethylene that is commonly used in low-cost
applications.
F F F F
n C C C C
F F F F n

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-89

Practice Problems
(1) In the hydrogen atom, Lyman reported a series of spectral lines with wavelengths of
1215.7, 1025.7, 972.5, and 949.7 Å, plus others of shorter wavelength. To what values of
nFINAL and nINITIAL do these lines correspond? (If you are having difficulty with this
problem, you should look up the term “Lyman series.”)

(2) The following table lists the energies (in kJ/mol) required to break the chemical bond in
certain gases found in our atmosphere. For each gas, calculate the maximum wavelength
(in nm) of light needed to break these bonds. Identify which part of the electromagnetic
spectrum each value corresponds.

Molecule Process Energy (kJ/mol)

N2 N2(g)  2N(g) 941
O3 O3(g)  O2(g) + O(g) 105
CF3Cl CF3Cl(g)  CF3(g) + Cl(g) 339

(3) (a) Determine the speed (m/sec) and wavelength (in pm) of electrons accelerated in an
electron microscope at an energy of 20.0 keV.
(b) Determine the momentum (in kgm/sec) and energy (in eV) of red light with a
wavelength of 720 nm.
(c) Determine the wavelength (in nm), momentum (in kgm/sec) and kinetic energy (in J)
of neutrons that are in thermal equilibrium at 300 K. (NOTE: use the equipartition
principle, that average kinetic energy is 3RT/2NA).

(4) Which of the following combinations of quantum numbers are allowed for an electron in
a one-electron atom? Which are not?

(a) n = 2, l = 2, m = 1, ms = 1/2
(b) n = 3, l = 1, m = 0, ms = 1/2
(c) n = 5, l = 1, m = 2, ms = 1/2
(d) n = 4, l = 1, m = 0, ms = 1/2
(e) n = 3, l = 2, m = 1, ms = 0
(f) n = 2, l = 0, m = 1, ms = 1/2
(g) n = 7, l = 2, m = 2, ms = 1/2
(h) n = 3, l = 3, m = 0, ms = 1/2

(5) Write down the ground state electronic configurations for

(a) Elements: C, Se, Fe, P, Tc, Ho;

(b) Ions: Be+, C, Ne2+, Mg+, P2+, As+, Cl, I

For each of these, identify the number of unpaired electrons.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-90

(6) Identify the atom or ion corresponding to each of the following descriptions:

(a) an atom with ground state electron configuration [Xe](4f)14(5d)6(6s)2;

(b) an ion with charge 1 and ground state electron configuration [He](2s)2(2p)6;
(c) anion with charge +5 and ground state electron configuration [Kr](4d)6.

(7) Quantum mechanics predicts that the energy of the ground state of the H atom is 13.6
eV relative to an isolated proton + an isolated electron. Consider several different
methods by which this energy can be measured:

(a) Calculate the longest wavelength of light that will ionize H atoms in their ground
state.
(b) Assume the atom is ionized by collision with an electron that transfers all its kinetic
energy to the atom in the ionization process. Calculate the speed of the electron (in
m/sec) before the collision.
(c) Calculate the temperature required to ionize a H atom in its ground state. This
temperature is given by the expression h = RT/NA (R = ideal gas constant; NA =
Avogadro’s number).

(8) For each of the following pairs of atoms or ions, state which you expect to have the larger
radius.

(a) Na or K
(b) Rb+ or Kr
(c) Cs or Cs+
(d) Cl or Ar
(e) K or Ca
(f) Sm or Sm3+
(g) Mg or Ca
(h) I or Xe
(i) Ge or As
(j) Sr+ or Rb
(k) O or S
(l) Co2+ or Ti2+
(m) Mn2+ or Mn4+
(n) Ca2+ or Sr2+

(9) The molecular orbital energy diagram for O2 and F2 (the one with no 2s-2p hybridization)
is also appropriate to describe the molecular orbital energies for heteroatomic molecules
like CO and NO.

(a) Use this diagram, and draw the molecular orbitals for the CO molecule.
(b) Use the diagram to predict the bond orders and numbers of unpaired electrons for BN,
CN, NO+, NO, NO, BF, and BO.

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-91

(10) Construct a molecular orbital energy diagram for the HF molecule. You may ignore the
valence 2s AO of fluorine, as it is very low in energy, and not heavily involved in
chemical bonding.

(11) For each of the following molecules or molecular ions, draw the Lewis structures, taking
into account resonance. For each Lewis structure, calculate the formal charge at each
atomic site, and construct a qualitative molecular orbital diagram (labeling bonding,
antibonding and nonbonding = lone pair orbitals). For each example, which orbital is the
HOMO and which orbital is the LUMO?

(a) O3 (ozone)
(b) CO2 (carbon dioxide)
(c) H2N-CH2-COOH (glycine: an amino acid)
(d) CH3NO2 (nitromethane)
(e) CH3CN (acetonitrile)
(f) HN3 (hydrazoic acid)

(12) Draw Lewis structures for two possible forms of hydrogen cyanide (HCN): (a) for H
bonded to the C atom; and (b) for H bonded to the N atom. Which isomer makes more
sense? Now use a qualitative molecular orbital diagram to explain your choice.

(13) For each of the following chemical formulas, write the Lewis structure, calculate formal
charges, identify the AO hybridizations at each “central” atom and label approximate
bond angles and distances. For (a) and (b), draw a qualitative molecular orbital energy
diagram, label all bonding, nonbonding and antibonding MOs, and identify the HOMO
and LUMO.

(a) Formic acid: HCOOH

(b) Nitrite ion: NO2
(c) Formate ion: HCOO
(d) Sulfur trioxide: SO3

(14) For each of the following formulas, use VSEPR to determine the molecular structure. For
(b) and (d), construct a qualitative molecular orbital energy diagram, label all bonding,
nonbonding and antibonding MOs, and identify the HOMO and LUMO.

(a) ICl4
(b) SF4
(c) AlCl3
(d) AlCl4

(15) Test the Ligand Close Packing (LCP) concept in the following models (the “law of
cosines” is helpful: c2 = a2 + b2 – 2ab cos C, where C = angle between sides a and b).

(a) Compare the nonbonded radii of H atoms in the sequence H2O, H2S, and H2Se.
Details of the molecular geometries are

-- Chemical Structure --
Unit #3 (Chemical Structure) 3-92

H2O: d(OH) = 95.7 pm; HOH = 104.5

H2S: d(SH) = 133.6 pm; HSH = 92.1
H2Se: d(SeH) = 146.0 pm; HSeH = 91.0
(b) Use the following molecular geometries of SH2, SF2, and SCl2 to predict bond angles
in HSF and HSCl.
SH2: d(SH) = 133.6 pm; HSH = 92.1
SF2: d(SF) = 159 pm; FSF = 98.3
SCl2: d(SCl) = 201 pm; ClSCl = 103

(16) Consider the case of hexatriene, CH2=CH–CH=CH–CH=CH2. Hexatriene is a conjugated

hydrocarbon containing three double bonds. For each double bond, one bond is formed by a 
overlap between electrons in sp2 orbitals on adjacent carbon atoms; the other bond is formed by a
 overlap between electrons in adjacent unhybridized p orbitals. The electrons in these bonds are
called “π electrons.” In a more correct description of this bonding based on a linear combination
of the unhybridized p atomic orbitals (LCAO), molecular orbitals can be constructed in which the
six p electrons are delocalized over the entire length of the hexatriene box.

The particle-in-the-box model we developed earlier can be used to discuss the electronic (i.e.,
UV/Vis) transitions in this molecule that can be measured with a common laboratory
spectrometer. Assume that the  electrons in hexatriene are free to move along the length of the
molecule. Approximate the energy levels of this system by using a one-dimensional box model
whose length is the length of the molecule plus one C–C single bond length. Use 1.54 Å as a C–
C and 1.35 Å as a C=C length. (1 Å, Ångstrom = 100 pm, 1 pm = 10-12 m). There are six 
electrons and only two of them may be placed in each energy level, according to the Pauli
principle. (An excellent and extremely accessible introduction to quantum mechanics is the text
by Hanna, Quantum Mechanics in Chemistry.) Using these six electrons to fill the three lowest
energy levels, calculate the following quantities:

a. The energy of the highest filled level.

b. The energy of the lowest unfilled level.
c. The difference in energy between the highest-energy filled and the lowest-energy unfilled
levels. This energy difference should be approximately equal to the energy of the longest
wavelength absorption band in the ultraviolet visible spectrum of the dye. Compare your
calculated energy with the experimental wavelength of maximum absorption max = 268 nm
(1 nm = 10–9 m).
d. Describe the bonding of the hexatriene molecule completely in terms of hybridization. That
is, draw a diagram illustrating the use of hybridization in the bonding.

(17) When are quantum effects important?

Consider a golf ball weighing 1.62 ounces moving in a one-dimensional shoe box of length 13.5
inches.

a. What is the velocity of the golf ball in units of cm/sec, cm/hr, cm/day, cm/year?

b. How big would Planck’s constant need to be in order for the golf ball to have a measureable
zero-point (kinetic) energy corresponding to a velocity of 1 cm/hr? (I.e., how much bigger than
the real Planck’s constant would this “macroscopic Planck’s constant” need to be in order to see
this effect?)

-- Chemical Structure --